Starting phenix.real_space_refine on Wed Jul 30 13:20:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qp6_4611/07_2025/6qp6_4611.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qp6_4611/07_2025/6qp6_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6qp6_4611/07_2025/6qp6_4611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qp6_4611/07_2025/6qp6_4611.map" model { file = "/net/cci-nas-00/data/ceres_data/6qp6_4611/07_2025/6qp6_4611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qp6_4611/07_2025/6qp6_4611.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 13.18, per 1000 atoms: 1.07 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: 3.05 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.37 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: 3.98 Time building geometry restraints manager: 3.46 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: 0.06 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: 0.730 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: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 35.900 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.600 ------------------------------------------------------------------------------- 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 : 5.89 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (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 TRP 0.026 0.003 TRP B 397 HIS 0.011 0.002 HIS A 830 PHE 0.038 0.003 PHE B 685 TYR 0.023 0.003 TYR B 580 ARG 0.007 0.001 ARG A 289 Details of bonding type rmsd hydrogen bonds : bond 0.12346 ( 736) hydrogen bonds : angle 5.94877 ( 2160) SS BOND : bond 0.01058 ( 8) SS BOND : angle 2.11681 ( 16) covalent geometry : bond 0.01019 (12652) covalent geometry : angle 1.06128 (17126) *********************** 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 : 1.426 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: 0.6878 (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: 0.8934 (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: 0.8898 (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: 0.2599 time to fit residues: 83.5414 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 : 1.288 ------------------------------------------------------------------------------- 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 124 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 0.2980 chunk 116 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 134 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.186329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145560 restraints weight = 14050.731| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.28 r_work: 0.3245 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1455 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= 0.139 Angle : 0.596 7.071 17142 Z= 0.324 Chirality : 0.041 0.151 1854 Planarity : 0.006 0.062 2120 Dihedral : 9.234 142.688 1696 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.57 % Allowed : 10.85 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.20), residues: 1442 helix: 0.10 (0.15), residues: 914 sheet: -1.64 (0.54), residues: 72 loop : -1.82 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 273 HIS 0.010 0.001 HIS A 655 PHE 0.015 0.001 PHE B 556 TYR 0.023 0.002 TYR A 406 ARG 0.004 0.000 ARG A 116 Details of bonding type rmsd hydrogen bonds : bond 0.05300 ( 736) hydrogen bonds : angle 5.03313 ( 2160) SS BOND : bond 0.00426 ( 8) SS BOND : angle 1.09138 ( 16) covalent geometry : bond 0.00282 (12652) covalent geometry : angle 0.59518 (17126) *********************** 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 203 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 1.441 Fit side-chains revert: symmetry clash REVERT: A 138 TYR cc_start: 0.7597 (m-80) cc_final: 0.7050 (m-80) REVERT: A 215 PHE cc_start: 0.8461 (t80) cc_final: 0.8232 (t80) REVERT: A 221 LYS cc_start: 0.6822 (mtmt) cc_final: 0.6309 (pttm) REVERT: A 360 ARG cc_start: 0.7975 (mtt-85) cc_final: 0.7560 (mtt90) REVERT: A 619 TRP cc_start: 0.7619 (t60) cc_final: 0.7147 (t-100) REVERT: B 138 TYR cc_start: 0.7426 (m-80) cc_final: 0.7074 (m-80) REVERT: B 221 LYS cc_start: 0.6888 (mtmt) cc_final: 0.6137 (pttm) REVERT: B 270 TYR cc_start: 0.8813 (t80) cc_final: 0.8587 (t80) REVERT: B 360 ARG cc_start: 0.7990 (mtt-85) cc_final: 0.7782 (mtt90) REVERT: B 407 GLU cc_start: 0.8014 (tt0) cc_final: 0.7417 (mt-10) REVERT: B 594 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7297 (mt-10) REVERT: B 619 TRP cc_start: 0.7677 (t60) cc_final: 0.7278 (t-100) REVERT: B 652 GLN cc_start: 0.8555 (mt0) cc_final: 0.8327 (mt0) REVERT: B 760 PHE cc_start: 0.8426 (m-80) cc_final: 0.8050 (m-80) REVERT: B 773 MET cc_start: 0.8892 (mmm) cc_final: 0.8304 (mmt) outliers start: 21 outliers final: 10 residues processed: 195 average time/residue: 0.2917 time to fit residues: 83.5467 Evaluate side-chains 164 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 1.456 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 45 optimal weight: 0.0060 chunk 15 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 92 optimal weight: 0.0870 overall best weight: 0.5174 ------------------------------------------------------------------------------- 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 B 559 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.184571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.146551 restraints weight = 14159.635| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.55 r_work: 0.3229 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12660 Z= 0.123 Angle : 0.542 6.900 17142 Z= 0.292 Chirality : 0.039 0.147 1854 Planarity : 0.005 0.053 2120 Dihedral : 8.867 142.817 1694 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.65 % Allowed : 13.10 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.21), residues: 1442 helix: 0.83 (0.16), residues: 918 sheet: -1.48 (0.55), residues: 72 loop : -1.62 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 273 HIS 0.008 0.001 HIS A 655 PHE 0.013 0.001 PHE B 556 TYR 0.055 0.001 TYR A 528 ARG 0.005 0.000 ARG B 542 Details of bonding type rmsd hydrogen bonds : bond 0.04720 ( 736) hydrogen bonds : angle 4.76488 ( 2160) SS BOND : bond 0.00594 ( 8) SS BOND : angle 0.74377 ( 16) covalent geometry : bond 0.00245 (12652) covalent geometry : angle 0.54208 (17126) *********************** 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: 22 poor density : 169 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.7972 (t0) REVERT: A 138 TYR cc_start: 0.7643 (m-80) cc_final: 0.7119 (m-80) REVERT: A 142 MET cc_start: 0.6894 (ptt) cc_final: 0.6416 (ptt) REVERT: A 221 LYS cc_start: 0.6962 (mtmt) cc_final: 0.6283 (pttm) REVERT: A 235 ARG cc_start: 0.7449 (ttt180) cc_final: 0.7222 (mtp180) REVERT: A 360 ARG cc_start: 0.7749 (mtt-85) cc_final: 0.7428 (mtt90) REVERT: A 528 TYR cc_start: 0.8010 (t80) cc_final: 0.7690 (t80) REVERT: A 619 TRP cc_start: 0.7490 (t60) cc_final: 0.7030 (t-100) REVERT: B 138 TYR cc_start: 0.7377 (m-80) cc_final: 0.6926 (m-80) REVERT: B 221 LYS cc_start: 0.6906 (mtmt) cc_final: 0.6551 (pttm) REVERT: B 270 TYR cc_start: 0.8669 (t80) cc_final: 0.8451 (t80) REVERT: B 407 GLU cc_start: 0.7875 (tt0) cc_final: 0.7302 (mt-10) REVERT: B 528 TYR cc_start: 0.7948 (t80) cc_final: 0.7665 (t80) REVERT: B 539 GLU cc_start: 0.7534 (pt0) cc_final: 0.7242 (pt0) REVERT: B 594 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7174 (mt-10) REVERT: B 619 TRP cc_start: 0.7588 (t60) cc_final: 0.7278 (t-100) REVERT: B 652 GLN cc_start: 0.8466 (mt0) cc_final: 0.8172 (mt0) REVERT: B 760 PHE cc_start: 0.8343 (m-80) cc_final: 0.8041 (m-80) outliers start: 22 outliers final: 15 residues processed: 183 average time/residue: 0.2204 time to fit residues: 60.3141 Evaluate side-chains 168 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 1.290 ------------------------------------------------------------------------------- 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 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 691 LEU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 769 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 68 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3958 r_free = 0.3958 target = 0.176154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.138285 restraints weight = 13993.187| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.31 r_work: 0.3218 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 12660 Z= 0.249 Angle : 0.639 7.072 17142 Z= 0.342 Chirality : 0.044 0.140 1854 Planarity : 0.005 0.053 2120 Dihedral : 9.078 138.599 1694 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.21), residues: 1442 helix: 0.91 (0.16), residues: 906 sheet: -0.19 (0.72), residues: 42 loop : -1.58 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 829 HIS 0.005 0.001 HIS A 830 PHE 0.026 0.002 PHE A 685 TYR 0.038 0.002 TYR B 528 ARG 0.004 0.001 ARG A 289 Details of bonding type rmsd hydrogen bonds : bond 0.05265 ( 736) hydrogen bonds : angle 4.86984 ( 2160) SS BOND : bond 0.00455 ( 8) SS BOND : angle 0.94266 ( 16) covalent geometry : bond 0.00583 (12652) covalent geometry : angle 0.63858 (17126) *********************** 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 188 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 ASN cc_start: 0.8454 (OUTLIER) cc_final: 0.8095 (t0) REVERT: A 122 LYS cc_start: 0.7325 (ptpt) cc_final: 0.7028 (pttt) REVERT: A 138 TYR cc_start: 0.7700 (m-80) cc_final: 0.7317 (m-80) REVERT: A 215 PHE cc_start: 0.8176 (t80) cc_final: 0.7931 (t80) REVERT: A 221 LYS cc_start: 0.6956 (mtmt) cc_final: 0.6304 (pttm) REVERT: A 235 ARG cc_start: 0.7746 (ttt180) cc_final: 0.7436 (mtp180) REVERT: A 346 ILE cc_start: 0.8742 (mm) cc_final: 0.8396 (mt) REVERT: A 360 ARG cc_start: 0.8080 (mtt-85) cc_final: 0.7863 (mtt90) REVERT: A 619 TRP cc_start: 0.7568 (t60) cc_final: 0.7085 (t-100) REVERT: A 661 LYS cc_start: 0.7508 (pttt) cc_final: 0.7025 (ptmm) REVERT: B 138 TYR cc_start: 0.7523 (m-80) cc_final: 0.7162 (m-80) REVERT: B 221 LYS cc_start: 0.6892 (mtmt) cc_final: 0.6448 (pttm) REVERT: B 346 ILE cc_start: 0.8673 (mm) cc_final: 0.8368 (mt) REVERT: B 407 GLU cc_start: 0.7913 (tt0) cc_final: 0.7378 (mt-10) REVERT: B 528 TYR cc_start: 0.8119 (t80) cc_final: 0.7502 (t80) REVERT: B 539 GLU cc_start: 0.7474 (pt0) cc_final: 0.7117 (pt0) REVERT: B 619 TRP cc_start: 0.7643 (t60) cc_final: 0.7318 (t-100) REVERT: B 652 GLN cc_start: 0.8612 (mt0) cc_final: 0.8351 (mt0) REVERT: B 760 PHE cc_start: 0.8421 (m-80) cc_final: 0.8115 (m-80) outliers start: 36 outliers final: 27 residues processed: 177 average time/residue: 0.2390 time to fit residues: 63.1726 Evaluate side-chains 175 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 1.287 ------------------------------------------------------------------------------- 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 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 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 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 228 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 682 VAL 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 127 optimal weight: 0.4980 chunk 52 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 62 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4031 r_free = 0.4031 target = 0.183581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.143628 restraints weight = 13981.157| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.24 r_work: 0.3195 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12660 Z= 0.128 Angle : 0.543 7.747 17142 Z= 0.293 Chirality : 0.040 0.134 1854 Planarity : 0.005 0.051 2120 Dihedral : 8.820 136.915 1694 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.47 % Allowed : 15.72 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.21), residues: 1442 helix: 1.19 (0.16), residues: 916 sheet: 0.11 (0.73), residues: 42 loop : -1.49 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 397 HIS 0.003 0.001 HIS A 655 PHE 0.018 0.001 PHE B 558 TYR 0.034 0.001 TYR B 528 ARG 0.004 0.000 ARG A 753 Details of bonding type rmsd hydrogen bonds : bond 0.04591 ( 736) hydrogen bonds : angle 4.73042 ( 2160) SS BOND : bond 0.00461 ( 8) SS BOND : angle 1.85172 ( 16) covalent geometry : bond 0.00267 (12652) covalent geometry : angle 0.54038 (17126) *********************** 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 186 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.8116 (t0) REVERT: A 142 MET cc_start: 0.6931 (ptt) cc_final: 0.6494 (ptt) REVERT: A 221 LYS cc_start: 0.6823 (mtmt) cc_final: 0.6183 (pttm) REVERT: A 235 ARG cc_start: 0.7504 (ttt180) cc_final: 0.7271 (mtp180) REVERT: A 594 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7218 (mt-10) REVERT: A 619 TRP cc_start: 0.7473 (t60) cc_final: 0.7019 (t-100) REVERT: A 661 LYS cc_start: 0.7385 (pttt) cc_final: 0.6834 (ptmm) REVERT: B 96 ARG cc_start: 0.7041 (mtp-110) cc_final: 0.6804 (mtp-110) REVERT: B 138 TYR cc_start: 0.7447 (m-80) cc_final: 0.6987 (m-80) REVERT: B 221 LYS cc_start: 0.6777 (mtmt) cc_final: 0.6329 (pttm) REVERT: B 407 GLU cc_start: 0.7836 (tt0) cc_final: 0.7306 (mt-10) REVERT: B 481 VAL cc_start: 0.6377 (OUTLIER) cc_final: 0.6172 (p) REVERT: B 517 SER cc_start: 0.8828 (p) cc_final: 0.8460 (p) REVERT: B 539 GLU cc_start: 0.7383 (pt0) cc_final: 0.7026 (pt0) REVERT: B 619 TRP cc_start: 0.7600 (t60) cc_final: 0.7250 (t-100) REVERT: B 652 GLN cc_start: 0.8474 (mt0) cc_final: 0.8171 (mt0) REVERT: B 760 PHE cc_start: 0.8365 (m-80) cc_final: 0.8084 (m-80) REVERT: B 773 MET cc_start: 0.8503 (mmt) cc_final: 0.8079 (mmt) outliers start: 33 outliers final: 21 residues processed: 176 average time/residue: 0.2389 time to fit residues: 62.7890 Evaluate side-chains 171 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 1.418 ------------------------------------------------------------------------------- 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 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 650 TRP 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 769 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 278 SER 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 769 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 135 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 144 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.178633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.140521 restraints weight = 14180.528| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.30 r_work: 0.3136 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12660 Z= 0.204 Angle : 0.599 7.704 17142 Z= 0.321 Chirality : 0.042 0.145 1854 Planarity : 0.005 0.049 2120 Dihedral : 8.804 135.418 1694 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.59 % Allowed : 14.82 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.22), residues: 1442 helix: 1.24 (0.16), residues: 904 sheet: 0.20 (0.72), residues: 42 loop : -1.42 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 829 HIS 0.004 0.001 HIS B 830 PHE 0.020 0.002 PHE B 685 TYR 0.035 0.002 TYR B 528 ARG 0.003 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.04927 ( 736) hydrogen bonds : angle 4.79238 ( 2160) SS BOND : bond 0.00349 ( 8) SS BOND : angle 1.90652 ( 16) covalent geometry : bond 0.00479 (12652) covalent geometry : angle 0.59613 (17126) *********************** 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 205 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 157 time to evaluate : 1.319 Fit side-chains revert: symmetry clash REVERT: A 104 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.8156 (t0) REVERT: A 122 LYS cc_start: 0.7302 (ptpt) cc_final: 0.7076 (pttt) REVERT: A 221 LYS cc_start: 0.6770 (mtmt) cc_final: 0.6170 (pttm) REVERT: A 235 ARG cc_start: 0.7494 (ttt180) cc_final: 0.7276 (mtp180) REVERT: A 346 ILE cc_start: 0.8637 (mm) cc_final: 0.8222 (mt) REVERT: A 619 TRP cc_start: 0.7524 (t60) cc_final: 0.7140 (t-100) REVERT: A 661 LYS cc_start: 0.7410 (pttt) cc_final: 0.6849 (ptmm) REVERT: A 749 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7751 (t0) REVERT: B 138 TYR cc_start: 0.7490 (m-80) cc_final: 0.7019 (m-80) REVERT: B 221 LYS cc_start: 0.6685 (mtmt) cc_final: 0.6312 (pttm) REVERT: B 346 ILE cc_start: 0.8574 (mm) cc_final: 0.8211 (mt) REVERT: B 407 GLU cc_start: 0.7868 (tt0) cc_final: 0.7321 (mt-10) REVERT: B 528 TYR cc_start: 0.8119 (t80) cc_final: 0.7445 (t80) REVERT: B 539 GLU cc_start: 0.7421 (pt0) cc_final: 0.7057 (pt0) REVERT: B 619 TRP cc_start: 0.7608 (t60) cc_final: 0.7181 (t-100) REVERT: B 652 GLN cc_start: 0.8495 (mt0) cc_final: 0.8195 (mt0) REVERT: B 749 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7693 (t0) REVERT: B 760 PHE cc_start: 0.8347 (m-80) cc_final: 0.8012 (m-80) outliers start: 48 outliers final: 32 residues processed: 189 average time/residue: 0.2234 time to fit residues: 62.9414 Evaluate side-chains 187 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 312 LEU 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 533 ILE 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 659 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 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 192 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 524 LEU 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 682 VAL Chi-restraints excluded: chain B residue 691 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 111 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 128 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.182641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.143360 restraints weight = 13996.622| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.31 r_work: 0.3179 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 12660 Z= 0.132 Angle : 0.546 7.013 17142 Z= 0.294 Chirality : 0.040 0.134 1854 Planarity : 0.005 0.049 2120 Dihedral : 8.640 134.332 1694 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.99 % Allowed : 15.42 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.22), residues: 1442 helix: 1.36 (0.16), residues: 912 sheet: 0.11 (0.70), residues: 42 loop : -1.43 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 397 HIS 0.002 0.001 HIS A 655 PHE 0.013 0.001 PHE A 556 TYR 0.033 0.001 TYR B 528 ARG 0.004 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04536 ( 736) hydrogen bonds : angle 4.69819 ( 2160) SS BOND : bond 0.00511 ( 8) SS BOND : angle 1.51130 ( 16) covalent geometry : bond 0.00286 (12652) covalent geometry : angle 0.54399 (17126) *********************** 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 202 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 LYS cc_start: 0.6775 (mtmt) cc_final: 0.6313 (pttm) REVERT: A 619 TRP cc_start: 0.7502 (t60) cc_final: 0.7143 (t-100) REVERT: A 661 LYS cc_start: 0.7394 (pttt) cc_final: 0.6855 (ptmm) REVERT: A 749 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7736 (t70) REVERT: B 221 LYS cc_start: 0.6715 (mtmt) cc_final: 0.6310 (pttm) REVERT: B 517 SER cc_start: 0.8840 (p) cc_final: 0.8491 (p) REVERT: B 539 GLU cc_start: 0.7318 (pt0) cc_final: 0.6924 (pt0) REVERT: B 619 TRP cc_start: 0.7640 (t60) cc_final: 0.7236 (t-100) REVERT: B 652 GLN cc_start: 0.8480 (mt0) cc_final: 0.8182 (mt0) REVERT: B 749 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7676 (t70) REVERT: B 760 PHE cc_start: 0.8344 (m-80) cc_final: 0.8058 (m-80) outliers start: 40 outliers final: 27 residues processed: 190 average time/residue: 0.2384 time to fit residues: 66.5076 Evaluate side-chains 182 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 1.317 ------------------------------------------------------------------------------- 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 613 MET 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 749 ASP Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 73 PHE 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 524 LEU Chi-restraints excluded: chain B residue 543 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 659 MET Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 691 LEU 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 860 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 47 optimal weight: 0.8980 chunk 112 optimal weight: 20.0000 chunk 93 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 122 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 108 optimal weight: 20.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.179709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.140078 restraints weight = 14089.994| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.41 r_work: 0.3223 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 12660 Z= 0.203 Angle : 0.609 7.542 17142 Z= 0.325 Chirality : 0.042 0.135 1854 Planarity : 0.005 0.048 2120 Dihedral : 8.650 133.190 1694 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.22 % Allowed : 15.79 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.22), residues: 1442 helix: 1.30 (0.16), residues: 902 sheet: 0.18 (0.69), residues: 42 loop : -1.41 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 829 HIS 0.004 0.001 HIS B 830 PHE 0.022 0.002 PHE B 558 TYR 0.040 0.002 TYR B 528 ARG 0.003 0.000 ARG B 810 Details of bonding type rmsd hydrogen bonds : bond 0.04873 ( 736) hydrogen bonds : angle 4.76197 ( 2160) SS BOND : bond 0.00385 ( 8) SS BOND : angle 1.68537 ( 16) covalent geometry : bond 0.00479 (12652) covalent geometry : angle 0.60675 (17126) *********************** 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 197 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.7433 (ptpt) cc_final: 0.7026 (pttt) REVERT: A 221 LYS cc_start: 0.6811 (mtmt) cc_final: 0.6419 (pttm) REVERT: A 346 ILE cc_start: 0.8617 (mm) cc_final: 0.8278 (mt) REVERT: A 619 TRP cc_start: 0.7610 (t60) cc_final: 0.7248 (t-100) REVERT: A 661 LYS cc_start: 0.7520 (pttt) cc_final: 0.7036 (ptmm) REVERT: A 749 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7897 (t0) REVERT: B 96 ARG cc_start: 0.7608 (mmm160) cc_final: 0.7092 (mtp-110) REVERT: B 98 ARG cc_start: 0.7744 (ttp-110) cc_final: 0.7327 (ttp-110) REVERT: B 221 LYS cc_start: 0.6839 (mtmt) cc_final: 0.6570 (pttm) REVERT: B 346 ILE cc_start: 0.8652 (mm) cc_final: 0.8320 (mt) REVERT: B 517 SER cc_start: 0.8920 (p) cc_final: 0.8555 (p) REVERT: B 528 TYR cc_start: 0.8121 (t80) cc_final: 0.7426 (t80) REVERT: B 539 GLU cc_start: 0.7363 (pt0) cc_final: 0.7023 (pt0) REVERT: B 619 TRP cc_start: 0.7624 (t60) cc_final: 0.7264 (t-100) REVERT: B 749 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7859 (t0) REVERT: B 760 PHE cc_start: 0.8448 (m-80) cc_final: 0.8147 (m-80) outliers start: 43 outliers final: 35 residues processed: 184 average time/residue: 0.2302 time to fit residues: 63.1645 Evaluate side-chains 188 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 1.492 ------------------------------------------------------------------------------- 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 312 LEU 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 613 MET Chi-restraints excluded: chain A residue 659 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 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 312 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 543 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 659 MET Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 691 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 18 optimal weight: 5.9990 chunk 135 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 652 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.182120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.141786 restraints weight = 14109.639| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.53 r_work: 0.3220 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 12660 Z= 0.158 Angle : 0.574 6.657 17142 Z= 0.307 Chirality : 0.041 0.133 1854 Planarity : 0.005 0.049 2120 Dihedral : 8.553 132.110 1694 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.14 % Allowed : 16.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.22), residues: 1442 helix: 1.38 (0.17), residues: 902 sheet: 0.09 (0.68), residues: 42 loop : -1.39 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 397 HIS 0.002 0.001 HIS A 830 PHE 0.019 0.001 PHE B 558 TYR 0.038 0.002 TYR B 528 ARG 0.004 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.04629 ( 736) hydrogen bonds : angle 4.70626 ( 2160) SS BOND : bond 0.00300 ( 8) SS BOND : angle 1.45275 ( 16) covalent geometry : bond 0.00364 (12652) covalent geometry : angle 0.57257 (17126) *********************** 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 196 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 2.783 Fit side-chains revert: symmetry clash REVERT: A 221 LYS cc_start: 0.6781 (mtmt) cc_final: 0.6404 (pttm) REVERT: A 268 LEU cc_start: 0.8803 (tt) cc_final: 0.8489 (pp) REVERT: A 517 SER cc_start: 0.8958 (p) cc_final: 0.8586 (p) REVERT: A 619 TRP cc_start: 0.7596 (t60) cc_final: 0.7236 (t-100) REVERT: A 661 LYS cc_start: 0.7523 (pttt) cc_final: 0.7031 (ptmm) REVERT: A 749 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7860 (t0) REVERT: B 96 ARG cc_start: 0.7506 (mmm160) cc_final: 0.7060 (mtp-110) REVERT: B 98 ARG cc_start: 0.7706 (ttp-110) cc_final: 0.7266 (ttp-110) REVERT: B 221 LYS cc_start: 0.6842 (mtmt) cc_final: 0.6441 (pttm) REVERT: B 268 LEU cc_start: 0.8857 (tt) cc_final: 0.8476 (pp) REVERT: B 517 SER cc_start: 0.8896 (p) cc_final: 0.8542 (p) REVERT: B 539 GLU cc_start: 0.7327 (pt0) cc_final: 0.6965 (pt0) REVERT: B 619 TRP cc_start: 0.7633 (t60) cc_final: 0.7269 (t-100) REVERT: B 749 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7838 (t0) REVERT: B 760 PHE cc_start: 0.8430 (m-80) cc_final: 0.8147 (m-80) REVERT: B 851 PHE cc_start: 0.8492 (m-80) cc_final: 0.8232 (m-80) outliers start: 42 outliers final: 32 residues processed: 185 average time/residue: 0.2782 time to fit residues: 77.6610 Evaluate side-chains 188 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 365 CYS 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 659 MET 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 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 196 TYR 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 524 LEU Chi-restraints excluded: chain B residue 543 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 659 MET Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 691 LEU 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 111 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 652 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.181646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.142868 restraints weight = 14147.592| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.55 r_work: 0.3258 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 12660 Z= 0.168 Angle : 0.583 6.548 17142 Z= 0.312 Chirality : 0.041 0.135 1854 Planarity : 0.005 0.050 2120 Dihedral : 8.544 131.782 1694 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.07 % Allowed : 16.39 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.22), residues: 1442 helix: 1.39 (0.17), residues: 902 sheet: 0.07 (0.68), residues: 42 loop : -1.38 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 397 HIS 0.003 0.001 HIS B 830 PHE 0.015 0.001 PHE A 556 TYR 0.042 0.002 TYR B 528 ARG 0.003 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.04664 ( 736) hydrogen bonds : angle 4.71166 ( 2160) SS BOND : bond 0.00287 ( 8) SS BOND : angle 1.47365 ( 16) covalent geometry : bond 0.00389 (12652) covalent geometry : angle 0.58126 (17126) ********************** 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 192 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 1.364 Fit side-chains REVERT: A 221 LYS cc_start: 0.6797 (mtmt) cc_final: 0.6384 (pttm) REVERT: A 268 LEU cc_start: 0.8783 (tt) cc_final: 0.8484 (pp) REVERT: A 517 SER cc_start: 0.8974 (p) cc_final: 0.8606 (p) REVERT: A 619 TRP cc_start: 0.7593 (t60) cc_final: 0.7252 (t-100) REVERT: A 661 LYS cc_start: 0.7523 (pttt) cc_final: 0.7140 (ptmm) REVERT: A 749 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7803 (t0) REVERT: B 96 ARG cc_start: 0.7316 (mmm160) cc_final: 0.7015 (mtp-110) REVERT: B 98 ARG cc_start: 0.7669 (ttp-110) cc_final: 0.7253 (ttp-110) REVERT: B 221 LYS cc_start: 0.6788 (mtmt) cc_final: 0.6506 (pttm) REVERT: B 268 LEU cc_start: 0.8877 (tt) cc_final: 0.8525 (pp) REVERT: B 517 SER cc_start: 0.8928 (p) cc_final: 0.8576 (p) REVERT: B 528 TYR cc_start: 0.8080 (t80) cc_final: 0.7482 (t80) REVERT: B 539 GLU cc_start: 0.7251 (pt0) cc_final: 0.6894 (pt0) REVERT: B 619 TRP cc_start: 0.7606 (t60) cc_final: 0.7269 (t-100) REVERT: B 749 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7797 (t0) REVERT: B 760 PHE cc_start: 0.8399 (m-80) cc_final: 0.8143 (m-80) REVERT: B 851 PHE cc_start: 0.8481 (m-80) cc_final: 0.8219 (m-80) outliers start: 41 outliers final: 34 residues processed: 181 average time/residue: 0.2339 time to fit residues: 62.9542 Evaluate side-chains 186 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 365 CYS 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 659 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 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 312 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 543 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 652 GLN Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 691 LEU 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 773 MET 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 43 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 652 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.180993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.140792 restraints weight = 14048.576| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.43 r_work: 0.3167 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.175 12660 Z= 0.211 Angle : 0.848 59.199 17142 Z= 0.485 Chirality : 0.044 0.801 1854 Planarity : 0.005 0.050 2120 Dihedral : 8.561 131.714 1694 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.99 % Allowed : 16.62 % Favored : 80.39 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.22), residues: 1442 helix: 1.38 (0.17), residues: 902 sheet: 0.06 (0.68), residues: 42 loop : -1.38 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 397 HIS 0.003 0.001 HIS A 830 PHE 0.015 0.001 PHE A 556 TYR 0.037 0.002 TYR B 528 ARG 0.003 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.04672 ( 736) hydrogen bonds : angle 4.72175 ( 2160) SS BOND : bond 0.00228 ( 8) SS BOND : angle 1.40854 ( 16) covalent geometry : bond 0.00450 (12652) covalent geometry : angle 0.84681 (17126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6065.52 seconds wall clock time: 106 minutes 21.92 seconds (6381.92 seconds total)