Starting phenix.real_space_refine on Wed Mar 4 09:06:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qp6_4611/03_2026/6qp6_4611.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qp6_4611/03_2026/6qp6_4611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6qp6_4611/03_2026/6qp6_4611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qp6_4611/03_2026/6qp6_4611.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qp6_4611/03_2026/6qp6_4611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qp6_4611/03_2026/6qp6_4611.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 P 2 5.49 5 S 80 5.16 5 C 8100 2.51 5 N 1978 2.21 5 O 2164 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 110 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12330 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 6124 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 33, 'TRANS': 707} Chain breaks: 9 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' CA': 3, 'P1O': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: B Time building chain proxies: 5.41, per 1000 atoms: 0.44 Number of scatterers: 12330 At special positions: 0 Unit cell: (88.044, 123.464, 112.332, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 80 16.00 P 2 15.00 O 2164 8.00 N 1978 7.00 C 8100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.02 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.01 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.02 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.01 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 572.5 milliseconds 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2824 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 64.0% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 89 through 108 removed outlier: 3.729A pdb=" N LYS A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN A 99 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASN A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 142 removed outlier: 3.845A pdb=" N MET A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 220 Processing helix chain 'A' and resid 232 through 239 removed outlier: 3.728A pdb=" N LEU A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.688A pdb=" N ILE A 279 " --> pdb=" O PRO A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 293 Processing helix chain 'A' and resid 293 through 327 removed outlier: 3.514A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 364 through 375 removed outlier: 3.513A pdb=" N LYS A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 408 removed outlier: 3.705A pdb=" N LEU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 427 removed outlier: 3.624A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 488 removed outlier: 3.531A pdb=" N ILE A 451 " --> pdb=" O CYS A 447 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 539 removed outlier: 3.827A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 539 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 573 removed outlier: 5.194A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 638 Proline residue: A 628 - end of helix Processing helix chain 'A' and resid 648 through 655 Processing helix chain 'A' and resid 664 through 680 Processing helix chain 'A' and resid 687 through 710 removed outlier: 4.033A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 747 removed outlier: 3.909A pdb=" N VAL A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 775 through 781 removed outlier: 3.611A pdb=" N LEU A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 802 Processing helix chain 'A' and resid 825 through 857 Processing helix chain 'A' and resid 861 through 875 Processing helix chain 'B' and resid 89 through 108 removed outlier: 3.729A pdb=" N LYS B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN B 99 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASN B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 142 removed outlier: 3.844A pdb=" N MET B 142 " --> pdb=" O TYR B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 220 Processing helix chain 'B' and resid 232 through 239 removed outlier: 3.728A pdb=" N LEU B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 275 through 279 removed outlier: 3.688A pdb=" N ILE B 279 " --> pdb=" O PRO B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 293 through 327 removed outlier: 3.513A pdb=" N LEU B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 330 No H-bonds generated for 'chain 'B' and resid 328 through 330' Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 364 through 375 removed outlier: 3.513A pdb=" N LYS B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 408 removed outlier: 3.704A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 427 removed outlier: 3.625A pdb=" N GLN B 426 " --> pdb=" O GLU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 488 removed outlier: 3.532A pdb=" N ILE B 451 " --> pdb=" O CYS B 447 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 539 removed outlier: 3.827A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B 539 " --> pdb=" O ILE B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 573 removed outlier: 5.194A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 638 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 648 through 655 Processing helix chain 'B' and resid 664 through 680 Processing helix chain 'B' and resid 687 through 710 removed outlier: 4.033A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 747 removed outlier: 3.909A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 775 through 781 removed outlier: 3.610A pdb=" N LEU B 781 " --> pdb=" O ILE B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 802 Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 875 Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 116 Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 148 removed outlier: 3.671A pdb=" N SER A 190 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 348 Processing sheet with id=AA4, first strand: chain 'A' and resid 782 through 785 Processing sheet with id=AA5, first strand: chain 'B' and resid 111 through 116 Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 148 removed outlier: 3.671A pdb=" N SER B 190 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 347 through 348 Processing sheet with id=AA8, first strand: chain 'B' and resid 782 through 785 736 hydrogen bonds defined for protein. 2160 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: 1.80 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1923 1.32 - 1.44: 3666 1.44 - 1.56: 6926 1.56 - 1.69: 15 1.69 - 1.81: 122 Bond restraints: 12652 Sorted by residual: bond pdb=" O3 P1O B1003 " pdb=" P1 P1O B1003 " ideal model delta sigma weight residual 1.648 1.776 -0.128 2.00e-02 2.50e+03 4.11e+01 bond pdb=" O3 P1O A1003 " pdb=" P1 P1O A1003 " ideal model delta sigma weight residual 1.648 1.776 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C19 P1O B1003 " pdb=" C20 P1O B1003 " ideal model delta sigma weight residual 1.502 1.583 -0.081 2.00e-02 2.50e+03 1.66e+01 bond pdb=" C19 P1O A1003 " pdb=" C20 P1O A1003 " ideal model delta sigma weight residual 1.502 1.583 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C19 P1O A1003 " pdb=" O7 P1O A1003 " ideal model delta sigma weight residual 1.331 1.409 -0.078 2.00e-02 2.50e+03 1.51e+01 ... (remaining 12647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 16063 2.01 - 4.03: 893 4.03 - 6.04: 127 6.04 - 8.06: 27 8.06 - 10.07: 16 Bond angle restraints: 17126 Sorted by residual: angle pdb=" N PRO A 763 " pdb=" CA PRO A 763 " pdb=" C PRO A 763 " ideal model delta sigma weight residual 110.70 117.09 -6.39 1.22e+00 6.72e-01 2.74e+01 angle pdb=" N PRO B 763 " pdb=" CA PRO B 763 " pdb=" C PRO B 763 " ideal model delta sigma weight residual 110.70 117.04 -6.34 1.22e+00 6.72e-01 2.70e+01 angle pdb=" C ARG A 191 " pdb=" N MET A 192 " pdb=" CA MET A 192 " ideal model delta sigma weight residual 121.54 130.92 -9.38 1.91e+00 2.74e-01 2.41e+01 angle pdb=" C ARG B 191 " pdb=" N MET B 192 " pdb=" CA MET B 192 " ideal model delta sigma weight residual 121.54 130.88 -9.34 1.91e+00 2.74e-01 2.39e+01 angle pdb=" CB GLU A 871 " pdb=" CG GLU A 871 " pdb=" CD GLU A 871 " ideal model delta sigma weight residual 112.60 119.60 -7.00 1.70e+00 3.46e-01 1.70e+01 ... (remaining 17121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.22: 7180 29.22 - 58.44: 278 58.44 - 87.66: 30 87.66 - 116.88: 0 116.88 - 146.10: 2 Dihedral angle restraints: 7490 sinusoidal: 3108 harmonic: 4382 Sorted by residual: dihedral pdb=" CB CYS B 596 " pdb=" SG CYS B 596 " pdb=" SG CYS B 601 " pdb=" CB CYS B 601 " ideal model delta sinusoidal sigma weight residual 93.00 151.43 -58.43 1 1.00e+01 1.00e-02 4.57e+01 dihedral pdb=" CB CYS A 596 " pdb=" SG CYS A 596 " pdb=" SG CYS A 601 " pdb=" CB CYS A 601 " ideal model delta sinusoidal sigma weight residual 93.00 151.39 -58.39 1 1.00e+01 1.00e-02 4.57e+01 dihedral pdb=" CA ARG A 191 " pdb=" C ARG A 191 " pdb=" N MET A 192 " pdb=" CA MET A 192 " ideal model delta harmonic sigma weight residual -180.00 -150.41 -29.59 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 7487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.022: 1852 1.022 - 2.044: 0 2.044 - 3.066: 0 3.066 - 4.087: 0 4.087 - 5.109: 2 Chirality restraints: 1854 Sorted by residual: chirality pdb=" C7 P1O B1003 " pdb=" C6 P1O B1003 " pdb=" C8 P1O B1003 " pdb=" O7 P1O B1003 " both_signs ideal model delta sigma weight residual False -2.35 2.76 -5.11 2.00e-01 2.50e+01 6.53e+02 chirality pdb=" C7 P1O A1003 " pdb=" C6 P1O A1003 " pdb=" C8 P1O A1003 " pdb=" O7 P1O A1003 " both_signs ideal model delta sigma weight residual False -2.35 2.76 -5.11 2.00e-01 2.50e+01 6.52e+02 chirality pdb=" CG LEU B 465 " pdb=" CB LEU B 465 " pdb=" CD1 LEU B 465 " pdb=" CD2 LEU B 465 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1851 not shown) Planarity restraints: 2120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 597 " 0.059 5.00e-02 4.00e+02 8.90e-02 1.27e+01 pdb=" N PRO B 598 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO B 598 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 598 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 597 " -0.059 5.00e-02 4.00e+02 8.88e-02 1.26e+01 pdb=" N PRO A 598 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 598 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 598 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 364 " -0.015 2.00e-02 2.50e+03 3.12e-02 9.75e+00 pdb=" C THR A 364 " 0.054 2.00e-02 2.50e+03 pdb=" O THR A 364 " -0.020 2.00e-02 2.50e+03 pdb=" N CYS A 365 " -0.018 2.00e-02 2.50e+03 ... (remaining 2117 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 119 2.56 - 3.14: 9402 3.14 - 3.73: 19680 3.73 - 4.31: 27113 4.31 - 4.90: 45713 Nonbonded interactions: 102027 Sorted by model distance: nonbonded pdb=" OH TYR A 406 " pdb=" OE2 GLU A 871 " model vdw 1.975 3.040 nonbonded pdb=" OH TYR B 406 " pdb=" OE2 GLU B 871 " model vdw 1.975 3.040 nonbonded pdb=" OG SER A 190 " pdb=" OD2 ASP A 194 " model vdw 2.228 3.040 nonbonded pdb=" OG SER B 190 " pdb=" OD2 ASP B 194 " model vdw 2.228 3.040 nonbonded pdb=" OG SER B 782 " pdb=" O ASP B 811 " model vdw 2.269 3.040 ... (remaining 102022 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.990 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 : 0.010 0.128 12660 Z= 0.442 Angle : 1.063 10.069 17142 Z= 0.590 Chirality : 0.178 5.109 1854 Planarity : 0.010 0.089 2120 Dihedral : 15.828 146.103 4642 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.45 % Allowed : 8.83 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.18), residues: 1442 helix: -1.53 (0.14), residues: 902 sheet: -1.24 (0.55), residues: 54 loop : -2.15 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 289 TYR 0.023 0.003 TYR B 580 PHE 0.038 0.003 PHE B 685 TRP 0.026 0.003 TRP B 397 HIS 0.011 0.002 HIS A 830 Details of bonding type rmsd covalent geometry : bond 0.01019 (12652) covalent geometry : angle 1.06128 (17126) SS BOND : bond 0.01058 ( 8) SS BOND : angle 2.11681 ( 16) hydrogen bonds : bond 0.12346 ( 736) hydrogen bonds : angle 5.94877 ( 2160) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 222 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 138 TYR cc_start: 0.7579 (m-80) cc_final: 0.7176 (m-80) REVERT: A 191 ARG cc_start: 0.6879 (mpp-170) cc_final: 0.6628 (mpp-170) REVERT: A 215 PHE cc_start: 0.8395 (t80) cc_final: 0.8166 (t80) REVERT: A 221 LYS cc_start: 0.7205 (mtmt) cc_final: 0.5959 (mmtt) REVERT: A 270 TYR cc_start: 0.8493 (t80) cc_final: 0.8281 (t80) REVERT: A 611 ILE cc_start: 0.8935 (mm) cc_final: 0.8723 (mm) REVERT: A 619 TRP cc_start: 0.7215 (t60) cc_final: 0.6977 (t-100) REVERT: B 108 HIS cc_start: 0.6240 (m90) cc_final: 0.6029 (m90) REVERT: B 138 TYR cc_start: 0.7468 (m-80) cc_final: 0.7038 (m-80) REVERT: B 221 LYS cc_start: 0.7356 (mtmt) cc_final: 0.6061 (mptt) REVERT: B 270 TYR cc_start: 0.8582 (t80) cc_final: 0.8327 (t80) REVERT: B 366 GLU cc_start: 0.7724 (tp30) cc_final: 0.7342 (mm-30) REVERT: B 542 ARG cc_start: 0.7312 (ptm-80) cc_final: 0.7100 (ptm-80) REVERT: B 594 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6955 (mt-10) REVERT: B 611 ILE cc_start: 0.8899 (mm) cc_final: 0.8681 (mm) REVERT: B 619 TRP cc_start: 0.7251 (t60) cc_final: 0.7049 (t-100) REVERT: B 760 PHE cc_start: 0.8351 (m-80) cc_final: 0.8129 (m-80) REVERT: B 773 MET cc_start: 0.8756 (mmm) cc_final: 0.8369 (mmt) outliers start: 6 outliers final: 2 residues processed: 226 average time/residue: 0.1135 time to fit residues: 36.5386 Evaluate side-chains 172 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 170 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain B residue 536 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 223 GLN A 283 GLN A 328 GLN A 549 ASN A 632 ASN A 652 GLN A 655 HIS A 710 GLN A 730 GLN A 814 ASN B 99 GLN B 143 HIS B 223 GLN B 283 GLN B 549 ASN B 632 ASN B 652 GLN B 655 HIS B 710 GLN B 730 GLN B 814 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.184602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145300 restraints weight = 14107.098| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.04 r_work: 0.3236 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12660 Z= 0.163 Angle : 0.611 7.095 17142 Z= 0.332 Chirality : 0.042 0.151 1854 Planarity : 0.006 0.063 2120 Dihedral : 9.241 141.488 1696 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.80 % Allowed : 10.70 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.20), residues: 1442 helix: 0.06 (0.15), residues: 918 sheet: -1.67 (0.54), residues: 72 loop : -1.91 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 116 TYR 0.021 0.002 TYR A 406 PHE 0.016 0.001 PHE B 556 TRP 0.017 0.001 TRP A 273 HIS 0.008 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00344 (12652) covalent geometry : angle 0.61008 (17126) SS BOND : bond 0.00296 ( 8) SS BOND : angle 1.28381 ( 16) hydrogen bonds : bond 0.05403 ( 736) hydrogen bonds : angle 5.04912 ( 2160) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 138 TYR cc_start: 0.7628 (m-80) cc_final: 0.7096 (m-80) REVERT: A 215 PHE cc_start: 0.8496 (t80) cc_final: 0.8260 (t80) REVERT: A 221 LYS cc_start: 0.6847 (mtmt) cc_final: 0.6321 (pttm) REVERT: A 360 ARG cc_start: 0.8127 (mtt-85) cc_final: 0.7723 (mtt90) REVERT: A 619 TRP cc_start: 0.7681 (t60) cc_final: 0.7220 (t-100) REVERT: B 138 TYR cc_start: 0.7462 (m-80) cc_final: 0.7138 (m-80) REVERT: B 221 LYS cc_start: 0.6946 (mtmt) cc_final: 0.6131 (pttm) REVERT: B 270 TYR cc_start: 0.8860 (t80) cc_final: 0.8626 (t80) REVERT: B 360 ARG cc_start: 0.8109 (mtt-85) cc_final: 0.7880 (mtt90) REVERT: B 407 GLU cc_start: 0.8087 (tt0) cc_final: 0.7517 (mt-10) REVERT: B 619 TRP cc_start: 0.7730 (t60) cc_final: 0.7336 (t-100) REVERT: B 652 GLN cc_start: 0.8606 (mt0) cc_final: 0.8388 (mt0) REVERT: B 760 PHE cc_start: 0.8476 (m-80) cc_final: 0.8121 (m-80) REVERT: B 773 MET cc_start: 0.8866 (mmm) cc_final: 0.8279 (mmt) outliers start: 24 outliers final: 12 residues processed: 192 average time/residue: 0.1043 time to fit residues: 29.2321 Evaluate side-chains 164 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 650 TRP Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 650 TRP Chi-restraints excluded: chain B residue 769 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 72 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 chunk 34 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.180057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.141956 restraints weight = 14150.369| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.54 r_work: 0.3238 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12660 Z= 0.171 Angle : 0.590 7.762 17142 Z= 0.318 Chirality : 0.041 0.142 1854 Planarity : 0.005 0.054 2120 Dihedral : 9.006 140.822 1694 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.32 % Allowed : 13.55 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.21), residues: 1442 helix: 0.77 (0.16), residues: 916 sheet: -1.14 (0.62), residues: 52 loop : -1.67 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 542 TYR 0.021 0.002 TYR A 528 PHE 0.018 0.002 PHE B 685 TRP 0.015 0.001 TRP B 397 HIS 0.006 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00383 (12652) covalent geometry : angle 0.59004 (17126) SS BOND : bond 0.00368 ( 8) SS BOND : angle 0.83877 ( 16) hydrogen bonds : bond 0.05080 ( 736) hydrogen bonds : angle 4.85177 ( 2160) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASN cc_start: 0.8343 (OUTLIER) cc_final: 0.8001 (t0) REVERT: A 138 TYR cc_start: 0.7717 (m-80) cc_final: 0.7274 (m-80) REVERT: A 142 MET cc_start: 0.7060 (ptt) cc_final: 0.6489 (ptt) REVERT: A 221 LYS cc_start: 0.7108 (mtmt) cc_final: 0.6421 (pttm) REVERT: A 235 ARG cc_start: 0.7669 (ttt180) cc_final: 0.7371 (mtp180) REVERT: A 360 ARG cc_start: 0.7979 (mtt-85) cc_final: 0.7581 (mtt90) REVERT: A 619 TRP cc_start: 0.7512 (t60) cc_final: 0.7085 (t-100) REVERT: B 138 TYR cc_start: 0.7528 (m-80) cc_final: 0.7160 (m-80) REVERT: B 221 LYS cc_start: 0.7061 (mtmt) cc_final: 0.6603 (pttm) REVERT: B 407 GLU cc_start: 0.7954 (tt0) cc_final: 0.7427 (mt-10) REVERT: B 619 TRP cc_start: 0.7673 (t60) cc_final: 0.7364 (t-100) REVERT: B 652 GLN cc_start: 0.8563 (mt0) cc_final: 0.8319 (mt0) REVERT: B 760 PHE cc_start: 0.8435 (m-80) cc_final: 0.8141 (m-80) REVERT: B 773 MET cc_start: 0.8853 (mmm) cc_final: 0.8190 (mmt) outliers start: 31 outliers final: 25 residues processed: 184 average time/residue: 0.0979 time to fit residues: 26.8438 Evaluate side-chains 176 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 780 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 145 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.180918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.142410 restraints weight = 14080.120| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.45 r_work: 0.3205 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12660 Z= 0.150 Angle : 0.552 6.386 17142 Z= 0.299 Chirality : 0.040 0.134 1854 Planarity : 0.005 0.052 2120 Dihedral : 8.911 138.525 1694 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.69 % Allowed : 15.19 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.21), residues: 1442 helix: 1.09 (0.16), residues: 916 sheet: -0.65 (0.68), residues: 52 loop : -1.55 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 48 TYR 0.019 0.001 TYR B 406 PHE 0.014 0.001 PHE B 556 TRP 0.014 0.001 TRP B 397 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00330 (12652) covalent geometry : angle 0.55147 (17126) SS BOND : bond 0.00351 ( 8) SS BOND : angle 0.94355 ( 16) hydrogen bonds : bond 0.04748 ( 736) hydrogen bonds : angle 4.78833 ( 2160) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.8102 (t0) REVERT: A 122 LYS cc_start: 0.7313 (ptpt) cc_final: 0.7003 (pttt) REVERT: A 142 MET cc_start: 0.7330 (ptt) cc_final: 0.6866 (ptt) REVERT: A 221 LYS cc_start: 0.6900 (mtmt) cc_final: 0.6244 (pttm) REVERT: A 235 ARG cc_start: 0.7623 (ttt180) cc_final: 0.7385 (mtp180) REVERT: A 481 VAL cc_start: 0.6326 (OUTLIER) cc_final: 0.6108 (p) REVERT: A 619 TRP cc_start: 0.7477 (t60) cc_final: 0.7017 (t-100) REVERT: B 138 TYR cc_start: 0.7411 (m-80) cc_final: 0.6978 (m-80) REVERT: B 221 LYS cc_start: 0.6806 (mtmt) cc_final: 0.6436 (pttm) REVERT: B 407 GLU cc_start: 0.7940 (tt0) cc_final: 0.7404 (mt-10) REVERT: B 481 VAL cc_start: 0.6567 (OUTLIER) cc_final: 0.6359 (p) REVERT: B 619 TRP cc_start: 0.7625 (t60) cc_final: 0.7279 (t-100) REVERT: B 760 PHE cc_start: 0.8389 (m-80) cc_final: 0.8108 (m-80) outliers start: 36 outliers final: 26 residues processed: 182 average time/residue: 0.1055 time to fit residues: 28.7209 Evaluate side-chains 172 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 134 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 128 optimal weight: 0.6980 chunk 9 optimal weight: 8.9990 chunk 138 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.176986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.137649 restraints weight = 14188.462| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.52 r_work: 0.3180 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 12660 Z= 0.245 Angle : 0.628 6.519 17142 Z= 0.336 Chirality : 0.044 0.139 1854 Planarity : 0.005 0.052 2120 Dihedral : 8.954 135.517 1694 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.74 % Allowed : 15.42 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.21), residues: 1442 helix: 1.06 (0.16), residues: 906 sheet: 0.04 (0.71), residues: 42 loop : -1.55 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 753 TYR 0.023 0.002 TYR B 406 PHE 0.022 0.002 PHE B 685 TRP 0.013 0.002 TRP A 829 HIS 0.005 0.001 HIS B 830 Details of bonding type rmsd covalent geometry : bond 0.00579 (12652) covalent geometry : angle 0.62616 (17126) SS BOND : bond 0.00350 ( 8) SS BOND : angle 1.82689 ( 16) hydrogen bonds : bond 0.05176 ( 736) hydrogen bonds : angle 4.87371 ( 2160) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 153 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.8144 (t0) REVERT: A 122 LYS cc_start: 0.7417 (ptpt) cc_final: 0.7105 (pttt) REVERT: A 221 LYS cc_start: 0.6944 (mtmt) cc_final: 0.6347 (pttm) REVERT: A 235 ARG cc_start: 0.7761 (ttt180) cc_final: 0.7495 (mtp180) REVERT: A 346 ILE cc_start: 0.8664 (mm) cc_final: 0.8348 (mt) REVERT: A 481 VAL cc_start: 0.6413 (OUTLIER) cc_final: 0.6205 (p) REVERT: A 619 TRP cc_start: 0.7658 (t60) cc_final: 0.7147 (t-100) REVERT: A 749 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7865 (t0) REVERT: B 96 ARG cc_start: 0.7329 (mtp-110) cc_final: 0.7084 (mtp-110) REVERT: B 138 TYR cc_start: 0.7513 (m-80) cc_final: 0.7118 (m-80) REVERT: B 221 LYS cc_start: 0.6801 (mtmt) cc_final: 0.6573 (pttm) REVERT: B 346 ILE cc_start: 0.8653 (mm) cc_final: 0.8329 (mt) REVERT: B 366 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7600 (mp0) REVERT: B 407 GLU cc_start: 0.7982 (tt0) cc_final: 0.7442 (mt-10) REVERT: B 481 VAL cc_start: 0.6549 (OUTLIER) cc_final: 0.6304 (p) REVERT: B 619 TRP cc_start: 0.7696 (t60) cc_final: 0.7309 (t-100) REVERT: B 749 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7840 (t0) REVERT: B 760 PHE cc_start: 0.8449 (m-80) cc_final: 0.8148 (m-80) outliers start: 50 outliers final: 32 residues processed: 189 average time/residue: 0.1000 time to fit residues: 28.6737 Evaluate side-chains 185 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 73 optimal weight: 10.0000 chunk 134 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 125 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 108 optimal weight: 20.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN B 652 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.181194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.142409 restraints weight = 14039.300| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.49 r_work: 0.3159 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12660 Z= 0.130 Angle : 0.550 7.522 17142 Z= 0.296 Chirality : 0.040 0.132 1854 Planarity : 0.005 0.051 2120 Dihedral : 8.737 134.448 1694 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.62 % Allowed : 16.54 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.22), residues: 1442 helix: 1.30 (0.16), residues: 914 sheet: 0.14 (0.71), residues: 42 loop : -1.50 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 753 TYR 0.021 0.001 TYR B 406 PHE 0.013 0.001 PHE B 556 TRP 0.015 0.001 TRP A 397 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00277 (12652) covalent geometry : angle 0.54775 (17126) SS BOND : bond 0.00466 ( 8) SS BOND : angle 1.66037 ( 16) hydrogen bonds : bond 0.04616 ( 736) hydrogen bonds : angle 4.75645 ( 2160) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.7351 (ptpt) cc_final: 0.7027 (pttt) REVERT: A 221 LYS cc_start: 0.6824 (mtmt) cc_final: 0.6359 (pttm) REVERT: A 481 VAL cc_start: 0.6278 (OUTLIER) cc_final: 0.6071 (p) REVERT: A 619 TRP cc_start: 0.7589 (t60) cc_final: 0.7092 (t-100) REVERT: A 749 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7787 (t70) REVERT: B 221 LYS cc_start: 0.6742 (mtmt) cc_final: 0.6467 (pttm) REVERT: B 407 GLU cc_start: 0.7959 (tt0) cc_final: 0.7452 (mt-10) REVERT: B 481 VAL cc_start: 0.6385 (OUTLIER) cc_final: 0.6180 (p) REVERT: B 517 SER cc_start: 0.8893 (p) cc_final: 0.8526 (p) REVERT: B 619 TRP cc_start: 0.7704 (t60) cc_final: 0.7305 (t-100) REVERT: B 749 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7694 (t70) REVERT: B 760 PHE cc_start: 0.8398 (m-80) cc_final: 0.8147 (m-80) REVERT: B 773 MET cc_start: 0.8541 (mmt) cc_final: 0.8099 (mmt) outliers start: 35 outliers final: 22 residues processed: 188 average time/residue: 0.1077 time to fit residues: 29.8667 Evaluate side-chains 176 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 14 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 11 optimal weight: 0.0070 chunk 103 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.182783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.142764 restraints weight = 14126.497| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.51 r_work: 0.3262 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 12660 Z= 0.133 Angle : 0.543 6.348 17142 Z= 0.291 Chirality : 0.040 0.130 1854 Planarity : 0.005 0.049 2120 Dihedral : 8.536 133.654 1694 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.84 % Allowed : 16.92 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.22), residues: 1442 helix: 1.43 (0.16), residues: 916 sheet: 0.11 (0.69), residues: 42 loop : -1.45 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.054 0.002 TYR B 528 PHE 0.013 0.001 PHE B 215 TRP 0.015 0.001 TRP A 397 HIS 0.002 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00293 (12652) covalent geometry : angle 0.54132 (17126) SS BOND : bond 0.00411 ( 8) SS BOND : angle 1.35492 ( 16) hydrogen bonds : bond 0.04449 ( 736) hydrogen bonds : angle 4.65648 ( 2160) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 122 LYS cc_start: 0.7339 (ptpt) cc_final: 0.7013 (pttt) REVERT: A 221 LYS cc_start: 0.6798 (mtmt) cc_final: 0.6375 (pttm) REVERT: A 268 LEU cc_start: 0.8774 (tt) cc_final: 0.8464 (pp) REVERT: A 517 SER cc_start: 0.8962 (p) cc_final: 0.8587 (p) REVERT: A 554 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7652 (ttpp) REVERT: A 619 TRP cc_start: 0.7579 (t60) cc_final: 0.7253 (t-100) REVERT: A 749 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7852 (t70) REVERT: B 142 MET cc_start: 0.6938 (ptt) cc_final: 0.6510 (ptt) REVERT: B 481 VAL cc_start: 0.6324 (OUTLIER) cc_final: 0.6116 (p) REVERT: B 517 SER cc_start: 0.8925 (p) cc_final: 0.8577 (p) REVERT: B 619 TRP cc_start: 0.7636 (t60) cc_final: 0.7320 (t-100) REVERT: B 749 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7791 (t70) REVERT: B 760 PHE cc_start: 0.8439 (m-80) cc_final: 0.8185 (m-80) REVERT: B 851 PHE cc_start: 0.8415 (m-80) cc_final: 0.8175 (m-80) outliers start: 38 outliers final: 25 residues processed: 191 average time/residue: 0.1006 time to fit residues: 29.2812 Evaluate side-chains 183 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 97 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 chunk 125 optimal weight: 0.0060 chunk 55 optimal weight: 0.4980 chunk 124 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.182654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.142870 restraints weight = 14123.011| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.44 r_work: 0.3177 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12660 Z= 0.140 Angle : 0.557 8.087 17142 Z= 0.299 Chirality : 0.040 0.188 1854 Planarity : 0.005 0.049 2120 Dihedral : 8.499 132.976 1694 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.92 % Allowed : 16.92 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.22), residues: 1442 helix: 1.41 (0.16), residues: 916 sheet: 0.14 (0.70), residues: 42 loop : -1.40 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 48 TYR 0.022 0.001 TYR A 528 PHE 0.014 0.001 PHE B 556 TRP 0.013 0.001 TRP A 397 HIS 0.002 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00313 (12652) covalent geometry : angle 0.55532 (17126) SS BOND : bond 0.00254 ( 8) SS BOND : angle 1.39899 ( 16) hydrogen bonds : bond 0.04491 ( 736) hydrogen bonds : angle 4.65337 ( 2160) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.7340 (ptpt) cc_final: 0.6945 (pttt) REVERT: A 221 LYS cc_start: 0.6647 (mtmt) cc_final: 0.6232 (pttm) REVERT: A 268 LEU cc_start: 0.8661 (tt) cc_final: 0.8349 (pp) REVERT: A 554 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7436 (ttpp) REVERT: A 619 TRP cc_start: 0.7483 (t60) cc_final: 0.7155 (t-100) REVERT: A 749 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7751 (t70) REVERT: B 98 ARG cc_start: 0.7637 (ttp-110) cc_final: 0.7107 (ttp-110) REVERT: B 142 MET cc_start: 0.7114 (ptt) cc_final: 0.6686 (ptt) REVERT: B 268 LEU cc_start: 0.8713 (tt) cc_final: 0.8431 (pp) REVERT: B 407 GLU cc_start: 0.7925 (tt0) cc_final: 0.7309 (mt-10) REVERT: B 481 VAL cc_start: 0.6219 (OUTLIER) cc_final: 0.6007 (p) REVERT: B 517 SER cc_start: 0.8880 (p) cc_final: 0.8535 (p) REVERT: B 619 TRP cc_start: 0.7586 (t60) cc_final: 0.7230 (t-100) REVERT: B 749 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7704 (t70) REVERT: B 760 PHE cc_start: 0.8363 (m-80) cc_final: 0.8102 (m-80) REVERT: B 851 PHE cc_start: 0.8331 (m-80) cc_final: 0.7920 (m-80) outliers start: 39 outliers final: 28 residues processed: 187 average time/residue: 0.0961 time to fit residues: 27.0702 Evaluate side-chains 183 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 11 optimal weight: 8.9990 chunk 121 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.177866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.133307 restraints weight = 14069.704| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.99 r_work: 0.3138 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 12660 Z= 0.247 Angle : 0.646 6.981 17142 Z= 0.345 Chirality : 0.044 0.162 1854 Planarity : 0.005 0.049 2120 Dihedral : 8.715 132.193 1694 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.07 % Allowed : 16.92 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.22), residues: 1442 helix: 1.17 (0.16), residues: 906 sheet: 0.10 (0.69), residues: 42 loop : -1.43 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 753 TYR 0.025 0.002 TYR A 528 PHE 0.021 0.002 PHE B 685 TRP 0.016 0.002 TRP A 829 HIS 0.004 0.001 HIS A 830 Details of bonding type rmsd covalent geometry : bond 0.00587 (12652) covalent geometry : angle 0.64398 (17126) SS BOND : bond 0.00346 ( 8) SS BOND : angle 1.77272 ( 16) hydrogen bonds : bond 0.05140 ( 736) hydrogen bonds : angle 4.85237 ( 2160) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.7444 (ptpt) cc_final: 0.7124 (pttt) REVERT: A 142 MET cc_start: 0.7069 (ptt) cc_final: 0.6427 (ptt) REVERT: A 221 LYS cc_start: 0.6721 (mtmt) cc_final: 0.6252 (pttm) REVERT: A 346 ILE cc_start: 0.8619 (mm) cc_final: 0.8226 (mt) REVERT: A 554 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7536 (ttpp) REVERT: A 619 TRP cc_start: 0.7669 (t60) cc_final: 0.7191 (t-100) REVERT: A 749 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7924 (t0) REVERT: B 98 ARG cc_start: 0.7625 (ttp-110) cc_final: 0.7082 (ttp-110) REVERT: B 346 ILE cc_start: 0.8651 (mm) cc_final: 0.8267 (mt) REVERT: B 481 VAL cc_start: 0.6266 (OUTLIER) cc_final: 0.6014 (p) REVERT: B 517 SER cc_start: 0.8862 (p) cc_final: 0.8498 (p) REVERT: B 554 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7644 (ttpp) REVERT: B 619 TRP cc_start: 0.7689 (t60) cc_final: 0.7239 (t-100) REVERT: B 749 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7891 (t0) REVERT: B 760 PHE cc_start: 0.8465 (m-80) cc_final: 0.8097 (m-80) outliers start: 41 outliers final: 29 residues processed: 181 average time/residue: 0.1007 time to fit residues: 27.3268 Evaluate side-chains 185 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 554 LYS Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 33 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 140 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.178947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.132269 restraints weight = 14150.929| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.00 r_work: 0.3235 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12660 Z= 0.205 Angle : 0.622 8.762 17142 Z= 0.331 Chirality : 0.043 0.149 1854 Planarity : 0.005 0.050 2120 Dihedral : 8.681 131.047 1694 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.99 % Allowed : 17.44 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.22), residues: 1442 helix: 1.18 (0.16), residues: 906 sheet: 0.10 (0.69), residues: 42 loop : -1.45 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 98 TYR 0.025 0.002 TYR B 406 PHE 0.017 0.002 PHE B 685 TRP 0.012 0.001 TRP B 273 HIS 0.003 0.001 HIS A 830 Details of bonding type rmsd covalent geometry : bond 0.00481 (12652) covalent geometry : angle 0.62041 (17126) SS BOND : bond 0.00329 ( 8) SS BOND : angle 1.57350 ( 16) hydrogen bonds : bond 0.04926 ( 736) hydrogen bonds : angle 4.81998 ( 2160) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.7637 (ptpt) cc_final: 0.7273 (pttt) REVERT: A 221 LYS cc_start: 0.6857 (mtmt) cc_final: 0.6448 (pttm) REVERT: A 554 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7677 (ttpp) REVERT: A 619 TRP cc_start: 0.7593 (t60) cc_final: 0.7075 (t-100) REVERT: A 749 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7805 (t0) REVERT: B 96 ARG cc_start: 0.7408 (mmm160) cc_final: 0.6754 (mtp-110) REVERT: B 98 ARG cc_start: 0.7710 (ttp-110) cc_final: 0.7240 (ttp-110) REVERT: B 268 LEU cc_start: 0.8837 (tt) cc_final: 0.8578 (pp) REVERT: B 346 ILE cc_start: 0.8595 (mm) cc_final: 0.8257 (mt) REVERT: B 407 GLU cc_start: 0.7953 (tt0) cc_final: 0.7417 (mt-10) REVERT: B 481 VAL cc_start: 0.6611 (OUTLIER) cc_final: 0.6345 (p) REVERT: B 517 SER cc_start: 0.8941 (p) cc_final: 0.8568 (p) REVERT: B 619 TRP cc_start: 0.7647 (t60) cc_final: 0.7271 (t-100) REVERT: B 749 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7788 (t0) REVERT: B 760 PHE cc_start: 0.8404 (m-80) cc_final: 0.8139 (m-80) outliers start: 40 outliers final: 33 residues processed: 177 average time/residue: 0.1084 time to fit residues: 28.4115 Evaluate side-chains 184 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 109 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 34 optimal weight: 20.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.182092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.137621 restraints weight = 14028.496| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.90 r_work: 0.3234 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12660 Z= 0.138 Angle : 0.568 9.411 17142 Z= 0.302 Chirality : 0.040 0.140 1854 Planarity : 0.005 0.051 2120 Dihedral : 8.494 130.741 1694 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.62 % Allowed : 17.96 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.22), residues: 1442 helix: 1.38 (0.17), residues: 904 sheet: 0.07 (0.70), residues: 42 loop : -1.37 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 48 TYR 0.021 0.001 TYR B 406 PHE 0.015 0.001 PHE A 558 TRP 0.015 0.001 TRP A 397 HIS 0.002 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00306 (12652) covalent geometry : angle 0.56708 (17126) SS BOND : bond 0.00245 ( 8) SS BOND : angle 1.31003 ( 16) hydrogen bonds : bond 0.04513 ( 736) hydrogen bonds : angle 4.71259 ( 2160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2900.31 seconds wall clock time: 50 minutes 27.86 seconds (3027.86 seconds total)