Starting phenix.real_space_refine on Thu Jun 5 19:33:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dun_47171/06_2025/9dun_47171.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dun_47171/06_2025/9dun_47171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dun_47171/06_2025/9dun_47171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dun_47171/06_2025/9dun_47171.map" model { file = "/net/cci-nas-00/data/ceres_data/9dun_47171/06_2025/9dun_47171.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dun_47171/06_2025/9dun_47171.cif" } resolution = 3.32 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= 0.000 sd= 0.065 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 50 5.16 5 C 4309 2.51 5 N 1133 2.21 5 O 1180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6672 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2041 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 22, 'TRANS': 238} Chain breaks: 7 Chain: "B" Number of atoms: 2021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2021 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 22, 'TRANS': 235} Chain breaks: 7 Chain: "C" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1028 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain breaks: 1 Chain: "D" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1032 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain breaks: 1 Chain: "E" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 258 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain breaks: 2 Chain: "F" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 292 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain breaks: 1 Time building chain proxies: 5.21, per 1000 atoms: 0.78 Number of scatterers: 6672 At special positions: 0 Unit cell: (83.391, 131.043, 69.312, 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 50 16.00 O 1180 8.00 N 1133 7.00 C 4309 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: 2.01 Conformation dependent library (CDL) restraints added in 1.2 seconds 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 6 sheets defined 38.0% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 312 through 327 removed outlier: 3.782A pdb=" N ASN A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N TYR A 318 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER A 326 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 364 removed outlier: 3.669A pdb=" N HIS A 364 " --> pdb=" O PRO A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 395 removed outlier: 3.713A pdb=" N LYS A 391 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'A' and resid 517 through 528 removed outlier: 3.749A pdb=" N ASP A 521 " --> pdb=" O LYS A 517 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A 523 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 524 " --> pdb=" O ARG A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 532 removed outlier: 3.589A pdb=" N GLN A 532 " --> pdb=" O SER A 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 529 through 532' Processing helix chain 'A' and resid 566 through 570 removed outlier: 3.644A pdb=" N ILE A 569 " --> pdb=" O PRO A 566 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU A 570 " --> pdb=" O THR A 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 566 through 570' Processing helix chain 'A' and resid 628 through 633 removed outlier: 4.205A pdb=" N ARG A 633 " --> pdb=" O PRO A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 651 removed outlier: 3.509A pdb=" N LEU A 650 " --> pdb=" O PRO A 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 327 removed outlier: 3.876A pdb=" N ASN B 325 " --> pdb=" O ASN B 321 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER B 326 " --> pdb=" O HIS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 395 removed outlier: 3.867A pdb=" N LYS B 391 " --> pdb=" O ILE B 387 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR B 392 " --> pdb=" O ASP B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 Processing helix chain 'B' and resid 519 through 529 removed outlier: 3.531A pdb=" N SER B 523 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE B 524 " --> pdb=" O ARG B 520 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 525 " --> pdb=" O ASP B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 532 No H-bonds generated for 'chain 'B' and resid 530 through 532' Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 569 through 574 removed outlier: 3.578A pdb=" N VAL B 573 " --> pdb=" O ILE B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 633 removed outlier: 4.324A pdb=" N ARG B 633 " --> pdb=" O PRO B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 651 removed outlier: 3.574A pdb=" N LEU B 650 " --> pdb=" O PRO B 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 60 removed outlier: 4.288A pdb=" N PHE C 59 " --> pdb=" O THR C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 69 Processing helix chain 'C' and resid 74 through 79 removed outlier: 4.037A pdb=" N SER C 78 " --> pdb=" O THR C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 104 removed outlier: 3.730A pdb=" N LYS C 98 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 100 " --> pdb=" O ARG C 96 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR C 103 " --> pdb=" O LEU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 126 Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.766A pdb=" N GLU C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 184 removed outlier: 3.598A pdb=" N CYS C 169 " --> pdb=" O HIS C 165 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N TYR C 174 " --> pdb=" O ARG C 170 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP C 178 " --> pdb=" O TYR C 174 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN C 181 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS C 182 " --> pdb=" O ASP C 178 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR C 183 " --> pdb=" O TRP C 179 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 58 removed outlier: 3.637A pdb=" N VAL D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR D 55 " --> pdb=" O TRP D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 69 Processing helix chain 'D' and resid 74 through 79 removed outlier: 3.983A pdb=" N SER D 78 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 102 removed outlier: 3.554A pdb=" N LYS D 98 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU D 100 " --> pdb=" O ARG D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 126 removed outlier: 3.591A pdb=" N LEU D 113 " --> pdb=" O ASP D 109 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 161 removed outlier: 3.805A pdb=" N LEU D 154 " --> pdb=" O TRP D 150 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG D 155 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS D 156 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS D 161 " --> pdb=" O GLU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 184 removed outlier: 3.871A pdb=" N ASP D 178 " --> pdb=" O TYR D 174 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP D 179 " --> pdb=" O PHE D 175 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU D 180 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN D 181 " --> pdb=" O LEU D 177 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS D 182 " --> pdb=" O ASP D 178 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 302 through 303 removed outlier: 3.536A pdb=" N VAL A 330 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A 349 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 370 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.311A pdb=" N ALA A 556 " --> pdb=" O LEU A 638 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL A 640 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG A 558 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS A 637 " --> pdb=" O CYS A 581 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 639 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A 576 " --> pdb=" O CYS A 611 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS A 611 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 301 through 303 removed outlier: 3.524A pdb=" N VAL B 330 " --> pdb=" O ILE B 353 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 347 through 350 removed outlier: 3.696A pdb=" N LYS B 370 " --> pdb=" O LEU B 350 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 556 through 559 removed outlier: 6.294A pdb=" N ALA B 556 " --> pdb=" O LEU B 638 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL B 640 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG B 558 " --> pdb=" O VAL B 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 577 through 578 168 hydrogen bonds defined for protein. 495 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: 1.83 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2103 1.34 - 1.46: 1359 1.46 - 1.58: 3298 1.58 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 6826 Sorted by residual: bond pdb=" CA ILE A 559 " pdb=" CB ILE A 559 " ideal model delta sigma weight residual 1.528 1.540 -0.012 1.34e-02 5.57e+03 7.85e-01 bond pdb=" N PRO A 628 " pdb=" CA PRO A 628 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.31e-02 5.83e+03 7.14e-01 bond pdb=" CA ASN B 592 " pdb=" CB ASN B 592 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 6.66e-01 bond pdb=" CB PRO F 651 " pdb=" CG PRO F 651 " ideal model delta sigma weight residual 1.492 1.531 -0.039 5.00e-02 4.00e+02 5.98e-01 bond pdb=" CA HIS C 63 " pdb=" C HIS C 63 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.34e-02 5.57e+03 5.48e-01 ... (remaining 6821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 8817 1.18 - 2.37: 354 2.37 - 3.55: 92 3.55 - 4.73: 18 4.73 - 5.91: 4 Bond angle restraints: 9285 Sorted by residual: angle pdb=" N ILE C 95 " pdb=" CA ILE C 95 " pdb=" C ILE C 95 " ideal model delta sigma weight residual 112.96 109.14 3.82 1.00e+00 1.00e+00 1.46e+01 angle pdb=" N LEU B 596 " pdb=" CA LEU B 596 " pdb=" C LEU B 596 " ideal model delta sigma weight residual 110.24 114.25 -4.01 1.30e+00 5.92e-01 9.51e+00 angle pdb=" N ILE A 518 " pdb=" CA ILE A 518 " pdb=" C ILE A 518 " ideal model delta sigma weight residual 111.58 108.32 3.26 1.06e+00 8.90e-01 9.48e+00 angle pdb=" C ASP D 61 " pdb=" N ASP D 62 " pdb=" CA ASP D 62 " ideal model delta sigma weight residual 121.54 126.67 -5.13 1.91e+00 2.74e-01 7.22e+00 angle pdb=" C ILE B 595 " pdb=" N LEU B 596 " pdb=" CA LEU B 596 " ideal model delta sigma weight residual 120.82 124.33 -3.51 1.47e+00 4.63e-01 5.69e+00 ... (remaining 9280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 3394 17.16 - 34.33: 434 34.33 - 51.49: 188 51.49 - 68.65: 36 68.65 - 85.82: 11 Dihedral angle restraints: 4063 sinusoidal: 1630 harmonic: 2433 Sorted by residual: dihedral pdb=" CA CYS C 60 " pdb=" C CYS C 60 " pdb=" N ASP C 61 " pdb=" CA ASP C 61 " ideal model delta harmonic sigma weight residual -180.00 -160.52 -19.48 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA THR B 625 " pdb=" C THR B 625 " pdb=" N PRO B 626 " pdb=" CA PRO B 626 " ideal model delta harmonic sigma weight residual 180.00 162.10 17.90 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA CYS D 60 " pdb=" C CYS D 60 " pdb=" N ASP D 61 " pdb=" CA ASP D 61 " ideal model delta harmonic sigma weight residual -180.00 -162.18 -17.82 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 4060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 588 0.028 - 0.056: 333 0.056 - 0.085: 93 0.085 - 0.113: 52 0.113 - 0.141: 14 Chirality restraints: 1080 Sorted by residual: chirality pdb=" CA ILE B 643 " pdb=" N ILE B 643 " pdb=" C ILE B 643 " pdb=" CB ILE B 643 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA VAL B 627 " pdb=" N VAL B 627 " pdb=" C VAL B 627 " pdb=" CB VAL B 627 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CB ILE A 595 " pdb=" CA ILE A 595 " pdb=" CG1 ILE A 595 " pdb=" CG2 ILE A 595 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 1077 not shown) Planarity restraints: 1149 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 661 " -0.041 5.00e-02 4.00e+02 6.32e-02 6.38e+00 pdb=" N PRO F 662 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO F 662 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 662 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 625 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO A 626 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 626 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 626 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 627 " 0.024 5.00e-02 4.00e+02 3.69e-02 2.17e+00 pdb=" N PRO A 628 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 628 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 628 " 0.020 5.00e-02 4.00e+02 ... (remaining 1146 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1345 2.78 - 3.31: 5854 3.31 - 3.84: 10407 3.84 - 4.37: 11885 4.37 - 4.90: 21207 Nonbonded interactions: 50698 Sorted by model distance: nonbonded pdb=" O SER A 427 " pdb=" OG SER A 427 " model vdw 2.246 3.040 nonbonded pdb=" OG SER F 636 " pdb=" N ALA F 637 " model vdw 2.246 3.120 nonbonded pdb=" OH TYR B 571 " pdb=" O ALA D 44 " model vdw 2.252 3.040 nonbonded pdb=" NZ LYS B 312 " pdb=" O THR B 407 " model vdw 2.256 3.120 nonbonded pdb=" NH1 ARG C 121 " pdb=" O LEU D 158 " model vdw 2.271 3.120 ... (remaining 50693 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 299 through 408 or resid 420 through 435 or resid 494 thro \ ugh 654)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 41 through 185) } ncs_group { reference = (chain 'E' and resid 636 through 674) selection = (chain 'F' and (resid 636 through 644 or resid 647 through 655 or resid 663 thro \ ugh 674)) } 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: 160.440 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.520 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:3.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 186.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 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 0.039 6826 Z= 0.126 Angle : 0.593 5.914 9285 Z= 0.316 Chirality : 0.041 0.141 1080 Planarity : 0.005 0.063 1149 Dihedral : 18.866 85.818 2479 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 4.63 % Allowed : 31.61 % Favored : 63.76 % 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: -2.65 (0.29), residues: 784 helix: -1.47 (0.30), residues: 265 sheet: -0.87 (0.55), residues: 89 loop : -2.18 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 647 HIS 0.006 0.001 HIS B 364 PHE 0.013 0.002 PHE B 394 TYR 0.011 0.001 TYR B 383 ARG 0.004 0.000 ARG C 171 Details of bonding type rmsd hydrogen bonds : bond 0.21650 ( 168) hydrogen bonds : angle 8.40560 ( 495) covalent geometry : bond 0.00286 ( 6826) covalent geometry : angle 0.59271 ( 9285) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 104 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 316 ASN cc_start: 0.6130 (OUTLIER) cc_final: 0.5928 (m-40) REVERT: A 339 GLN cc_start: 0.8087 (mp10) cc_final: 0.7561 (mt0) REVERT: A 369 GLN cc_start: 0.7330 (tt0) cc_final: 0.6955 (mt0) REVERT: A 391 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.6852 (mmmt) REVERT: A 419 LEU cc_start: 0.4042 (OUTLIER) cc_final: 0.3176 (pt) REVERT: A 517 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7400 (tmtt) REVERT: A 610 ILE cc_start: 0.7335 (OUTLIER) cc_final: 0.6870 (mm) REVERT: B 339 GLN cc_start: 0.8138 (mp10) cc_final: 0.7610 (mt0) REVERT: B 369 GLN cc_start: 0.7160 (tt0) cc_final: 0.6885 (mt0) REVERT: B 383 TYR cc_start: 0.7400 (OUTLIER) cc_final: 0.6707 (m-80) REVERT: B 391 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.6875 (mmmt) REVERT: B 520 ARG cc_start: 0.7226 (mtm110) cc_final: 0.6765 (mtp-110) REVERT: C 162 LYS cc_start: 0.8164 (mtpt) cc_final: 0.7629 (mtpt) REVERT: D 48 ARG cc_start: 0.7096 (mmt90) cc_final: 0.6561 (mmt180) REVERT: D 83 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7876 (mt-10) REVERT: D 162 LYS cc_start: 0.8340 (mtpt) cc_final: 0.7795 (mtpt) REVERT: D 179 TRP cc_start: 0.6026 (OUTLIER) cc_final: 0.4677 (t60) REVERT: E 666 MET cc_start: 0.7337 (mmm) cc_final: 0.6891 (mmm) outliers start: 35 outliers final: 25 residues processed: 135 average time/residue: 0.2166 time to fit residues: 40.0168 Evaluate side-chains 134 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 383 TYR Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain E residue 665 LEU Chi-restraints excluded: chain F residue 643 GLU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 652 LEU Chi-restraints excluded: chain F residue 665 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 41 optimal weight: 0.0060 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 0.0020 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 73 optimal weight: 0.2980 overall best weight: 0.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN B 316 ASN B 385 ASN B 549 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.221730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.193520 restraints weight = 6650.144| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 1.82 r_work: 0.3966 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3827 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6826 Z= 0.107 Angle : 0.563 6.080 9285 Z= 0.289 Chirality : 0.041 0.148 1080 Planarity : 0.005 0.051 1149 Dihedral : 8.756 57.947 964 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 5.82 % Allowed : 30.69 % Favored : 63.49 % 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: -2.45 (0.30), residues: 784 helix: -1.02 (0.30), residues: 293 sheet: -0.66 (0.52), residues: 93 loop : -2.38 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 179 HIS 0.006 0.001 HIS B 364 PHE 0.013 0.001 PHE A 362 TYR 0.013 0.001 TYR B 383 ARG 0.005 0.000 ARG B 612 Details of bonding type rmsd hydrogen bonds : bond 0.03344 ( 168) hydrogen bonds : angle 5.63519 ( 495) covalent geometry : bond 0.00242 ( 6826) covalent geometry : angle 0.56299 ( 9285) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 105 time to evaluate : 0.772 Fit side-chains REVERT: A 339 GLN cc_start: 0.7974 (mp10) cc_final: 0.7358 (mt0) REVERT: A 369 GLN cc_start: 0.7341 (tt0) cc_final: 0.6929 (mt0) REVERT: A 383 TYR cc_start: 0.7442 (OUTLIER) cc_final: 0.6716 (m-80) REVERT: A 391 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.6593 (mmmt) REVERT: A 517 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7250 (tmtt) REVERT: B 339 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7399 (mt0) REVERT: B 369 GLN cc_start: 0.7207 (tt0) cc_final: 0.6953 (mt0) REVERT: B 520 ARG cc_start: 0.7088 (mtm110) cc_final: 0.6638 (mtp-110) REVERT: B 592 ASN cc_start: 0.5640 (t0) cc_final: 0.5425 (t0) REVERT: C 50 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7172 (mt-10) REVERT: C 162 LYS cc_start: 0.8064 (mtpt) cc_final: 0.7478 (mtpt) REVERT: D 83 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7709 (mt-10) REVERT: D 162 LYS cc_start: 0.8226 (mtpt) cc_final: 0.7470 (mtpt) REVERT: D 179 TRP cc_start: 0.5877 (OUTLIER) cc_final: 0.4786 (t60) REVERT: E 666 MET cc_start: 0.7361 (mmm) cc_final: 0.6919 (mmm) outliers start: 44 outliers final: 22 residues processed: 143 average time/residue: 0.2130 time to fit residues: 41.1118 Evaluate side-chains 123 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain E residue 652 LEU Chi-restraints excluded: chain F residue 643 GLU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 665 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 54 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN A 636 ASN B 385 ASN B 433 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.217065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.188755 restraints weight = 6803.198| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 1.83 r_work: 0.3918 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3776 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6826 Z= 0.141 Angle : 0.589 6.329 9285 Z= 0.298 Chirality : 0.043 0.164 1080 Planarity : 0.005 0.059 1149 Dihedral : 8.405 59.261 939 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.35 % Favored : 88.65 % Rotamer: Outliers : 5.56 % Allowed : 30.95 % Favored : 63.49 % 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: -2.45 (0.29), residues: 784 helix: -0.94 (0.30), residues: 288 sheet: -0.44 (0.54), residues: 87 loop : -2.47 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 577 HIS 0.007 0.001 HIS B 364 PHE 0.014 0.002 PHE A 362 TYR 0.014 0.002 TYR A 332 ARG 0.003 0.000 ARG B 612 Details of bonding type rmsd hydrogen bonds : bond 0.03800 ( 168) hydrogen bonds : angle 5.23353 ( 495) covalent geometry : bond 0.00343 ( 6826) covalent geometry : angle 0.58852 ( 9285) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 100 time to evaluate : 0.748 Fit side-chains REVERT: A 339 GLN cc_start: 0.7968 (mp10) cc_final: 0.7389 (mt0) REVERT: A 369 GLN cc_start: 0.7375 (tt0) cc_final: 0.6966 (mt0) REVERT: A 383 TYR cc_start: 0.7601 (OUTLIER) cc_final: 0.6768 (m-80) REVERT: A 391 LYS cc_start: 0.7150 (OUTLIER) cc_final: 0.6180 (mmtt) REVERT: A 517 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7346 (tmtt) REVERT: A 519 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7208 (mp) REVERT: B 339 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7393 (mt0) REVERT: B 369 GLN cc_start: 0.7249 (tt0) cc_final: 0.6975 (mt0) REVERT: B 520 ARG cc_start: 0.7150 (mtm110) cc_final: 0.6708 (mtp-110) REVERT: C 50 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7327 (mt-10) REVERT: C 162 LYS cc_start: 0.8112 (mtpt) cc_final: 0.7484 (mtpt) REVERT: C 174 TYR cc_start: 0.6107 (m-80) cc_final: 0.5887 (m-80) REVERT: D 162 LYS cc_start: 0.8199 (mtpt) cc_final: 0.7440 (mtpt) REVERT: D 179 TRP cc_start: 0.5914 (OUTLIER) cc_final: 0.4801 (t60) REVERT: F 671 ASP cc_start: 0.6555 (t0) cc_final: 0.6342 (t0) outliers start: 42 outliers final: 24 residues processed: 136 average time/residue: 0.2477 time to fit residues: 46.4564 Evaluate side-chains 126 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 549 GLN Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain E residue 652 LEU Chi-restraints excluded: chain F residue 643 GLU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 665 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 19 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 chunk 1 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 66 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 385 ASN B 385 ASN D 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.218959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.190580 restraints weight = 6776.768| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 1.83 r_work: 0.3931 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3790 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6826 Z= 0.114 Angle : 0.551 6.333 9285 Z= 0.281 Chirality : 0.042 0.151 1080 Planarity : 0.005 0.059 1149 Dihedral : 8.209 58.208 937 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Rotamer: Outliers : 5.69 % Allowed : 30.95 % Favored : 63.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.33 (0.30), residues: 784 helix: -0.79 (0.30), residues: 289 sheet: -0.22 (0.56), residues: 87 loop : -2.49 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 577 HIS 0.005 0.001 HIS B 364 PHE 0.013 0.002 PHE A 362 TYR 0.012 0.001 TYR B 383 ARG 0.005 0.000 ARG B 612 Details of bonding type rmsd hydrogen bonds : bond 0.03217 ( 168) hydrogen bonds : angle 4.96585 ( 495) covalent geometry : bond 0.00275 ( 6826) covalent geometry : angle 0.55112 ( 9285) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 102 time to evaluate : 1.078 Fit side-chains REVERT: A 339 GLN cc_start: 0.7947 (mp10) cc_final: 0.7367 (mt0) REVERT: A 369 GLN cc_start: 0.7368 (tt0) cc_final: 0.6981 (mt0) REVERT: A 383 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.6741 (m-80) REVERT: A 391 LYS cc_start: 0.7075 (OUTLIER) cc_final: 0.6135 (mmtt) REVERT: A 517 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7203 (tmtt) REVERT: A 519 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7134 (mp) REVERT: B 339 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7381 (mt0) REVERT: B 369 GLN cc_start: 0.7243 (tt0) cc_final: 0.6968 (mt0) REVERT: B 520 ARG cc_start: 0.7132 (mtm110) cc_final: 0.6700 (mtp-110) REVERT: B 558 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7050 (ttt90) REVERT: C 50 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7253 (mt-10) REVERT: C 162 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7460 (mtpt) REVERT: C 184 TYR cc_start: 0.5709 (t80) cc_final: 0.5408 (t80) REVERT: D 83 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7680 (mt-10) REVERT: D 162 LYS cc_start: 0.8164 (mtpt) cc_final: 0.7418 (mtpt) REVERT: D 170 ARG cc_start: 0.6896 (mtt180) cc_final: 0.6677 (mtt180) REVERT: D 179 TRP cc_start: 0.5942 (OUTLIER) cc_final: 0.4821 (t60) REVERT: F 671 ASP cc_start: 0.6660 (t0) cc_final: 0.6367 (t0) outliers start: 43 outliers final: 28 residues processed: 138 average time/residue: 0.2736 time to fit residues: 51.3714 Evaluate side-chains 134 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 558 ARG Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 66 GLN Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain E residue 664 GLU Chi-restraints excluded: chain F residue 643 GLU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 665 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 12 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 HIS A 385 ASN B 385 ASN D 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.217089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.188467 restraints weight = 6780.014| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 1.83 r_work: 0.3910 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6826 Z= 0.136 Angle : 0.573 5.913 9285 Z= 0.291 Chirality : 0.042 0.162 1080 Planarity : 0.005 0.062 1149 Dihedral : 8.480 59.796 937 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.97 % Favored : 89.03 % Rotamer: Outliers : 5.95 % Allowed : 30.82 % Favored : 63.23 % 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: -2.37 (0.29), residues: 784 helix: -0.80 (0.30), residues: 289 sheet: -0.33 (0.57), residues: 87 loop : -2.51 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 577 HIS 0.006 0.001 HIS B 364 PHE 0.014 0.002 PHE A 362 TYR 0.014 0.002 TYR A 332 ARG 0.004 0.000 ARG B 612 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 168) hydrogen bonds : angle 4.90762 ( 495) covalent geometry : bond 0.00331 ( 6826) covalent geometry : angle 0.57330 ( 9285) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 106 time to evaluate : 1.444 Fit side-chains REVERT: A 339 GLN cc_start: 0.7962 (mp10) cc_final: 0.7349 (mt0) REVERT: A 369 GLN cc_start: 0.7279 (tt0) cc_final: 0.6896 (mt0) REVERT: A 383 TYR cc_start: 0.7473 (OUTLIER) cc_final: 0.6725 (m-80) REVERT: A 391 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6216 (mmtt) REVERT: A 517 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7401 (tmtt) REVERT: A 519 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7205 (mp) REVERT: B 339 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7354 (mt0) REVERT: B 369 GLN cc_start: 0.7145 (tt0) cc_final: 0.6881 (mt0) REVERT: B 520 ARG cc_start: 0.7156 (mtm110) cc_final: 0.6713 (mtp-110) REVERT: B 558 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7070 (ttt90) REVERT: C 50 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7266 (mt-10) REVERT: C 150 TRP cc_start: 0.7805 (t-100) cc_final: 0.7123 (t60) REVERT: C 162 LYS cc_start: 0.8254 (mtpt) cc_final: 0.7642 (mtpt) REVERT: D 162 LYS cc_start: 0.8153 (mtpt) cc_final: 0.7463 (mtpt) REVERT: D 179 TRP cc_start: 0.5985 (OUTLIER) cc_final: 0.4849 (t60) outliers start: 45 outliers final: 31 residues processed: 145 average time/residue: 0.3503 time to fit residues: 70.0004 Evaluate side-chains 141 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 103 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 558 ARG Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 66 GLN Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain E residue 652 LEU Chi-restraints excluded: chain E residue 664 GLU Chi-restraints excluded: chain E residue 665 LEU Chi-restraints excluded: chain F residue 643 GLU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 665 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 25 optimal weight: 0.8980 chunk 21 optimal weight: 0.0170 chunk 23 optimal weight: 0.0870 chunk 32 optimal weight: 0.0020 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 0.0020 chunk 11 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.2012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 385 ASN B 385 ASN D 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.221119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.192202 restraints weight = 6674.858| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 1.90 r_work: 0.3954 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6826 Z= 0.093 Angle : 0.521 5.654 9285 Z= 0.269 Chirality : 0.041 0.148 1080 Planarity : 0.005 0.061 1149 Dihedral : 8.212 59.679 935 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.82 % Favored : 90.05 % Rotamer: Outliers : 6.08 % Allowed : 29.76 % Favored : 64.15 % 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: -2.06 (0.30), residues: 784 helix: -0.42 (0.31), residues: 289 sheet: -0.28 (0.56), residues: 93 loop : -2.43 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 577 HIS 0.004 0.001 HIS A 430 PHE 0.011 0.001 PHE A 362 TYR 0.009 0.001 TYR B 383 ARG 0.004 0.000 ARG B 612 Details of bonding type rmsd hydrogen bonds : bond 0.02790 ( 168) hydrogen bonds : angle 4.62781 ( 495) covalent geometry : bond 0.00217 ( 6826) covalent geometry : angle 0.52062 ( 9285) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 107 time to evaluate : 1.673 Fit side-chains REVERT: A 339 GLN cc_start: 0.7834 (mp10) cc_final: 0.7238 (mt0) REVERT: A 369 GLN cc_start: 0.7263 (tt0) cc_final: 0.7023 (mt0) REVERT: A 383 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.6698 (m-80) REVERT: A 391 LYS cc_start: 0.6985 (OUTLIER) cc_final: 0.6074 (mmtt) REVERT: A 517 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7203 (tmtt) REVERT: A 519 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6979 (mp) REVERT: A 558 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.6842 (ttt90) REVERT: B 339 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7276 (mt0) REVERT: B 369 GLN cc_start: 0.7258 (tt0) cc_final: 0.6847 (mt0) REVERT: B 520 ARG cc_start: 0.7040 (mtm110) cc_final: 0.6615 (mtp-110) REVERT: B 558 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.6950 (ttt90) REVERT: C 50 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7160 (mt-10) REVERT: C 162 LYS cc_start: 0.8116 (mtpt) cc_final: 0.7496 (mtpt) REVERT: D 83 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7547 (mt-10) REVERT: D 162 LYS cc_start: 0.8096 (mtpt) cc_final: 0.7415 (mtpt) REVERT: D 179 TRP cc_start: 0.5954 (OUTLIER) cc_final: 0.4770 (t60) outliers start: 46 outliers final: 26 residues processed: 146 average time/residue: 0.3738 time to fit residues: 76.1638 Evaluate side-chains 136 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 558 ARG Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 558 ARG Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain E residue 652 LEU Chi-restraints excluded: chain F residue 643 GLU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 665 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 0.0770 chunk 13 optimal weight: 4.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN B 325 ASN B 385 ASN D 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.215090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.187375 restraints weight = 6880.514| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 1.82 r_work: 0.3891 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6826 Z= 0.176 Angle : 0.627 5.645 9285 Z= 0.317 Chirality : 0.045 0.173 1080 Planarity : 0.006 0.066 1149 Dihedral : 8.508 59.952 935 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.48 % Favored : 88.39 % Rotamer: Outliers : 5.95 % Allowed : 30.29 % Favored : 63.76 % 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: -2.38 (0.29), residues: 784 helix: -0.75 (0.30), residues: 289 sheet: -0.45 (0.57), residues: 86 loop : -2.53 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 577 HIS 0.007 0.001 HIS B 364 PHE 0.015 0.002 PHE B 342 TYR 0.017 0.002 TYR A 332 ARG 0.004 0.000 ARG A 435 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 168) hydrogen bonds : angle 4.86814 ( 495) covalent geometry : bond 0.00435 ( 6826) covalent geometry : angle 0.62732 ( 9285) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 108 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: A 339 GLN cc_start: 0.8063 (mp10) cc_final: 0.7431 (mt0) REVERT: A 369 GLN cc_start: 0.7269 (tt0) cc_final: 0.6870 (mt0) REVERT: A 371 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.6278 (tpp) REVERT: A 383 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.6809 (m-80) REVERT: A 391 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.6343 (mmtt) REVERT: A 517 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7576 (tmtt) REVERT: A 519 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7326 (mp) REVERT: B 339 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7380 (mt0) REVERT: B 369 GLN cc_start: 0.7189 (tt0) cc_final: 0.6893 (mt0) REVERT: B 371 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.6603 (tpp) REVERT: B 382 ASN cc_start: 0.8275 (m-40) cc_final: 0.7916 (m-40) REVERT: B 520 ARG cc_start: 0.7234 (mtm110) cc_final: 0.6802 (mtp-110) REVERT: B 558 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7182 (ttt90) REVERT: C 162 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7675 (mtpt) REVERT: D 162 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7545 (mtpt) REVERT: D 179 TRP cc_start: 0.6072 (OUTLIER) cc_final: 0.4874 (t60) outliers start: 45 outliers final: 26 residues processed: 143 average time/residue: 0.2383 time to fit residues: 47.6968 Evaluate side-chains 142 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 558 ARG Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 66 GLN Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain F residue 643 GLU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 665 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 4 optimal weight: 0.0270 chunk 71 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 77 optimal weight: 0.2980 chunk 79 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 chunk 69 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 57 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 385 ASN B 385 ASN D 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.218837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.191444 restraints weight = 6793.025| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 1.80 r_work: 0.3934 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6826 Z= 0.110 Angle : 0.566 7.193 9285 Z= 0.291 Chirality : 0.042 0.155 1080 Planarity : 0.006 0.071 1149 Dihedral : 7.944 58.036 931 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.95 % Favored : 89.92 % Rotamer: Outliers : 5.29 % Allowed : 30.82 % Favored : 63.89 % 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: -2.14 (0.30), residues: 784 helix: -0.45 (0.31), residues: 289 sheet: -0.47 (0.56), residues: 87 loop : -2.44 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 577 HIS 0.005 0.001 HIS B 430 PHE 0.016 0.002 PHE B 434 TYR 0.011 0.001 TYR A 332 ARG 0.003 0.000 ARG B 612 Details of bonding type rmsd hydrogen bonds : bond 0.03114 ( 168) hydrogen bonds : angle 4.69829 ( 495) covalent geometry : bond 0.00268 ( 6826) covalent geometry : angle 0.56626 ( 9285) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 99 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 339 GLN cc_start: 0.8023 (mp10) cc_final: 0.7412 (mt0) REVERT: A 369 GLN cc_start: 0.7321 (tt0) cc_final: 0.6918 (mt0) REVERT: A 371 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.6027 (tpp) REVERT: A 383 TYR cc_start: 0.7624 (OUTLIER) cc_final: 0.6809 (m-80) REVERT: A 391 LYS cc_start: 0.7115 (OUTLIER) cc_final: 0.6139 (mmtt) REVERT: A 517 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7247 (tmtt) REVERT: A 519 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7113 (mp) REVERT: A 558 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7053 (ttt90) REVERT: B 339 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7411 (mt0) REVERT: B 369 GLN cc_start: 0.7436 (tt0) cc_final: 0.6951 (mt0) REVERT: B 371 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.6284 (tpp) REVERT: B 520 ARG cc_start: 0.7112 (mtm110) cc_final: 0.6720 (mtp-110) REVERT: B 558 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7133 (ttt90) REVERT: C 150 TRP cc_start: 0.7806 (t-100) cc_final: 0.7085 (t60) REVERT: C 162 LYS cc_start: 0.8197 (mtpt) cc_final: 0.7578 (mtpt) REVERT: D 83 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7703 (mp0) REVERT: D 162 LYS cc_start: 0.8091 (mtpt) cc_final: 0.7417 (mtpt) REVERT: D 179 TRP cc_start: 0.6028 (OUTLIER) cc_final: 0.4747 (t60) REVERT: E 666 MET cc_start: 0.7502 (mmm) cc_final: 0.6998 (mmm) REVERT: E 668 GLU cc_start: 0.2370 (OUTLIER) cc_final: 0.1758 (mp0) REVERT: F 673 MET cc_start: 0.7026 (mtt) cc_final: 0.6594 (mtt) outliers start: 40 outliers final: 27 residues processed: 132 average time/residue: 0.2040 time to fit residues: 36.0644 Evaluate side-chains 137 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 99 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 558 ARG Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 558 ARG Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 66 GLN Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain E residue 668 GLU Chi-restraints excluded: chain F residue 643 GLU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 665 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 26 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN B 385 ASN D 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.216993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.187631 restraints weight = 6886.156| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 1.92 r_work: 0.3907 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6826 Z= 0.137 Angle : 0.585 6.817 9285 Z= 0.299 Chirality : 0.043 0.152 1080 Planarity : 0.006 0.069 1149 Dihedral : 7.936 57.318 931 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.84 % Favored : 89.03 % Rotamer: Outliers : 5.82 % Allowed : 30.29 % Favored : 63.89 % 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: -2.17 (0.30), residues: 784 helix: -0.52 (0.30), residues: 289 sheet: -0.53 (0.57), residues: 87 loop : -2.42 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 577 HIS 0.005 0.001 HIS B 364 PHE 0.022 0.002 PHE B 434 TYR 0.013 0.002 TYR A 332 ARG 0.003 0.000 ARG B 612 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 168) hydrogen bonds : angle 4.72210 ( 495) covalent geometry : bond 0.00339 ( 6826) covalent geometry : angle 0.58549 ( 9285) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 100 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 339 GLN cc_start: 0.7970 (mp10) cc_final: 0.7356 (mt0) REVERT: A 369 GLN cc_start: 0.7212 (tt0) cc_final: 0.6822 (mt0) REVERT: A 371 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.6098 (tpp) REVERT: A 383 TYR cc_start: 0.7544 (OUTLIER) cc_final: 0.6824 (m-80) REVERT: A 391 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6195 (mmtt) REVERT: A 517 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7367 (tmtt) REVERT: A 519 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7125 (mp) REVERT: B 339 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7353 (mt0) REVERT: B 369 GLN cc_start: 0.7190 (tt0) cc_final: 0.6895 (mt0) REVERT: B 371 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.6432 (tpp) REVERT: B 382 ASN cc_start: 0.8206 (m-40) cc_final: 0.7844 (m-40) REVERT: B 408 MET cc_start: 0.7621 (mtt) cc_final: 0.7257 (mtt) REVERT: B 520 ARG cc_start: 0.7150 (mtm110) cc_final: 0.6729 (mtp-110) REVERT: B 558 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7088 (ttt90) REVERT: C 162 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7643 (mtpt) REVERT: D 106 LEU cc_start: 0.4001 (OUTLIER) cc_final: 0.3282 (pp) REVERT: D 162 LYS cc_start: 0.8106 (mtpt) cc_final: 0.7454 (mtpt) REVERT: D 179 TRP cc_start: 0.6014 (OUTLIER) cc_final: 0.4747 (t60) REVERT: E 668 GLU cc_start: 0.2478 (OUTLIER) cc_final: 0.1811 (mp0) REVERT: F 673 MET cc_start: 0.7110 (mtt) cc_final: 0.6641 (mtt) outliers start: 44 outliers final: 30 residues processed: 136 average time/residue: 0.1938 time to fit residues: 35.5784 Evaluate side-chains 142 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 100 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 558 ARG Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 66 GLN Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain E residue 652 LEU Chi-restraints excluded: chain E residue 668 GLU Chi-restraints excluded: chain F residue 643 GLU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 665 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 44 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 385 ASN B 385 ASN D 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.217124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.187125 restraints weight = 6951.826| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 1.99 r_work: 0.3895 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6826 Z= 0.135 Angle : 0.588 6.695 9285 Z= 0.300 Chirality : 0.043 0.152 1080 Planarity : 0.006 0.069 1149 Dihedral : 7.873 56.440 931 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.71 % Favored : 89.16 % Rotamer: Outliers : 5.95 % Allowed : 30.03 % Favored : 64.02 % 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: -2.18 (0.30), residues: 784 helix: -0.51 (0.30), residues: 289 sheet: -0.54 (0.57), residues: 87 loop : -2.43 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 577 HIS 0.005 0.001 HIS B 364 PHE 0.019 0.002 PHE B 434 TYR 0.013 0.001 TYR A 332 ARG 0.004 0.000 ARG B 612 Details of bonding type rmsd hydrogen bonds : bond 0.03330 ( 168) hydrogen bonds : angle 4.70021 ( 495) covalent geometry : bond 0.00333 ( 6826) covalent geometry : angle 0.58823 ( 9285) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 101 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 339 GLN cc_start: 0.7962 (mp10) cc_final: 0.7350 (mt0) REVERT: A 364 HIS cc_start: 0.7840 (OUTLIER) cc_final: 0.7554 (p90) REVERT: A 369 GLN cc_start: 0.7194 (tt0) cc_final: 0.6809 (mt0) REVERT: A 371 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.6090 (tpp) REVERT: A 383 TYR cc_start: 0.7573 (OUTLIER) cc_final: 0.6847 (m-80) REVERT: A 391 LYS cc_start: 0.7145 (OUTLIER) cc_final: 0.6173 (mmtt) REVERT: A 517 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7370 (tmtt) REVERT: A 519 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7139 (mp) REVERT: A 558 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7034 (ttt90) REVERT: B 339 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7342 (mt0) REVERT: B 369 GLN cc_start: 0.7385 (tt0) cc_final: 0.6874 (mt0) REVERT: B 371 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.6440 (tpp) REVERT: B 382 ASN cc_start: 0.8258 (m-40) cc_final: 0.7851 (m-40) REVERT: B 408 MET cc_start: 0.7613 (mtt) cc_final: 0.7276 (mtt) REVERT: B 520 ARG cc_start: 0.7144 (mtm110) cc_final: 0.6722 (mtp-110) REVERT: B 558 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7096 (ttt90) REVERT: C 162 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7632 (mtpt) REVERT: D 106 LEU cc_start: 0.4049 (OUTLIER) cc_final: 0.3330 (pp) REVERT: D 162 LYS cc_start: 0.8176 (mtpt) cc_final: 0.7434 (mtpt) REVERT: D 179 TRP cc_start: 0.6012 (OUTLIER) cc_final: 0.4727 (t60) REVERT: E 666 MET cc_start: 0.7583 (mmm) cc_final: 0.7025 (mmm) REVERT: E 668 GLU cc_start: 0.2434 (OUTLIER) cc_final: 0.1751 (mp0) REVERT: F 643 GLU cc_start: 0.6222 (OUTLIER) cc_final: 0.5083 (pp20) REVERT: F 673 MET cc_start: 0.7064 (mtt) cc_final: 0.6587 (mtt) outliers start: 45 outliers final: 29 residues processed: 139 average time/residue: 0.1987 time to fit residues: 37.0038 Evaluate side-chains 143 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 99 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 558 ARG Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 558 ARG Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 66 GLN Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain E residue 652 LEU Chi-restraints excluded: chain E residue 668 GLU Chi-restraints excluded: chain F residue 643 GLU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 665 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 63 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 chunk 74 optimal weight: 4.9990 chunk 18 optimal weight: 0.0870 chunk 41 optimal weight: 0.0970 chunk 25 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN B 385 ASN C 160 HIS D 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.219304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.192406 restraints weight = 6914.657| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 1.77 r_work: 0.3937 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6826 Z= 0.107 Angle : 0.558 6.524 9285 Z= 0.287 Chirality : 0.042 0.151 1080 Planarity : 0.006 0.068 1149 Dihedral : 7.706 55.797 931 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.95 % Favored : 89.92 % Rotamer: Outliers : 5.69 % Allowed : 30.42 % Favored : 63.89 % 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: -2.00 (0.30), residues: 784 helix: -0.33 (0.31), residues: 289 sheet: -0.46 (0.58), residues: 87 loop : -2.34 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 577 HIS 0.005 0.001 HIS B 430 PHE 0.016 0.002 PHE B 434 TYR 0.011 0.001 TYR A 383 ARG 0.003 0.000 ARG D 67 Details of bonding type rmsd hydrogen bonds : bond 0.03044 ( 168) hydrogen bonds : angle 4.59648 ( 495) covalent geometry : bond 0.00258 ( 6826) covalent geometry : angle 0.55776 ( 9285) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4866.85 seconds wall clock time: 88 minutes 20.93 seconds (5300.93 seconds total)