Starting phenix.real_space_refine on Fri Sep 11 23:57:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6qp6_4611/09_2026/6qp6_4611.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qp6_4611/09_2026/6qp6_4611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6qp6_4611/09_2026/6qp6_4611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qp6_4611/09_2026/6qp6_4611.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6qp6_4611/09_2026/6qp6_4611.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6qp6_4611/09_2026/6qp6_4611.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qp6_4611/09_2026/6qp6_4611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qp6_4611/09_2026/6qp6_4611.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 P 2 5.49 5 S 80 5.16 5 C 8100 2.51 5 N 1978 2.21 5 O 2164 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 110 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12330 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 6124 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 33, 'TRANS': 707} Chain breaks: 9 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' CA': 3, 'P1O': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: B Time building chain proxies: 5.46, per 1000 atoms: 0.44 Number of scatterers: 12330 At special positions: 0 Unit cell: (88.044, 123.464, 112.332, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 80 16.00 P 2 15.00 O 2164 8.00 N 1978 7.00 C 8100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.02 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.01 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.02 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.01 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 469.5 milliseconds 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2824 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 64.0% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 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: 2.28 Time building geometry restraints manager: 1.32 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 - 17.51: 6538 17.51 - 35.02: 745 35.02 - 52.54: 131 52.54 - 70.05: 48 70.05 - 87.56: 10 Dihedral angle restraints: 7472 sinusoidal: 3090 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 7469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.022: 1852 1.022 - 2.044: 0 2.044 - 3.066: 0 3.066 - 4.087: 0 4.087 - 5.109: 2 Chirality restraints: 1854 Sorted by residual: chirality pdb=" C7 P1O B1003 " pdb=" C6 P1O B1003 " pdb=" C8 P1O B1003 " pdb=" O7 P1O B1003 " both_signs ideal model delta sigma weight residual False -2.35 2.76 -5.11 2.00e-01 2.50e+01 6.53e+02 chirality pdb=" C7 P1O A1003 " pdb=" C6 P1O A1003 " pdb=" C8 P1O A1003 " pdb=" O7 P1O A1003 " both_signs ideal model delta sigma weight residual False -2.35 2.76 -5.11 2.00e-01 2.50e+01 6.52e+02 chirality pdb=" CG LEU B 465 " pdb=" CB LEU B 465 " pdb=" CD1 LEU B 465 " pdb=" CD2 LEU B 465 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1851 not shown) Planarity restraints: 2120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 597 " 0.059 5.00e-02 4.00e+02 8.90e-02 1.27e+01 pdb=" N PRO B 598 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO B 598 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 598 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 597 " -0.059 5.00e-02 4.00e+02 8.88e-02 1.26e+01 pdb=" N PRO A 598 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 598 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 598 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 364 " -0.015 2.00e-02 2.50e+03 3.12e-02 9.75e+00 pdb=" C THR A 364 " 0.054 2.00e-02 2.50e+03 pdb=" O THR A 364 " -0.020 2.00e-02 2.50e+03 pdb=" N CYS A 365 " -0.018 2.00e-02 2.50e+03 ... (remaining 2117 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 119 2.56 - 3.14: 9402 3.14 - 3.73: 19680 3.73 - 4.31: 27113 4.31 - 4.90: 45713 Nonbonded interactions: 102027 Sorted by model distance: nonbonded pdb=" OH TYR A 406 " pdb=" OE2 GLU A 871 " model vdw 1.975 3.040 nonbonded pdb=" OH TYR B 406 " pdb=" OE2 GLU B 871 " model vdw 1.975 3.040 nonbonded pdb=" OG SER A 190 " pdb=" OD2 ASP A 194 " model vdw 2.228 3.040 nonbonded pdb=" OG SER B 190 " pdb=" OD2 ASP B 194 " model vdw 2.228 3.040 nonbonded pdb=" OG SER B 782 " pdb=" O ASP B 811 " model vdw 2.269 3.040 ... (remaining 102022 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 14.480 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 : 15.494 87.560 4624 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.45 % Allowed : 8.83 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.18), residues: 1442 helix: -1.53 (0.14), residues: 902 sheet: -1.24 (0.55), residues: 54 loop : -2.15 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 289 TYR 0.023 0.003 TYR B 580 PHE 0.038 0.003 PHE B 685 TRP 0.026 0.003 TRP B 397 HIS 0.011 0.002 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.01019 / 0.44 (12652) covalent geometry : angle 1.06128 / 0.59 (17126) SS BOND : bond 0.01058 / 0.54 ( 8) SS BOND : angle 2.11681 / 1.42 ( 16) hydrogen bonds : bond 0.12346 / 8.39 ( 736) hydrogen bonds : angle 5.94877 / 4.04 ( 2160) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 222 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 138 TYR cc_start: 0.7579 (m-80) cc_final: 0.7176 (m-80) REVERT: A 191 ARG cc_start: 0.6879 (mpp-170) cc_final: 0.6628 (mpp-170) REVERT: A 215 PHE cc_start: 0.8395 (t80) cc_final: 0.8166 (t80) REVERT: A 221 LYS cc_start: 0.7205 (mtmt) cc_final: 0.5959 (mmtt) REVERT: A 270 TYR cc_start: 0.8493 (t80) cc_final: 0.8281 (t80) REVERT: A 611 ILE cc_start: 0.8935 (mm) cc_final: 0.8723 (mm) REVERT: A 619 TRP cc_start: 0.7215 (t60) cc_final: 0.6977 (t-100) REVERT: B 108 HIS cc_start: 0.6240 (m90) cc_final: 0.6029 (m90) REVERT: B 138 TYR cc_start: 0.7468 (m-80) cc_final: 0.7038 (m-80) REVERT: B 221 LYS cc_start: 0.7356 (mtmt) cc_final: 0.6061 (mptt) REVERT: B 270 TYR cc_start: 0.8582 (t80) cc_final: 0.8327 (t80) REVERT: B 366 GLU cc_start: 0.7724 (tp30) cc_final: 0.7342 (mm-30) REVERT: B 542 ARG cc_start: 0.7312 (ptm-80) cc_final: 0.7100 (ptm-80) REVERT: B 594 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6955 (mt-10) REVERT: B 611 ILE cc_start: 0.8899 (mm) cc_final: 0.8681 (mm) REVERT: B 619 TRP cc_start: 0.7251 (t60) cc_final: 0.7049 (t-100) REVERT: B 760 PHE cc_start: 0.8351 (m-80) cc_final: 0.8129 (m-80) REVERT: B 773 MET cc_start: 0.8756 (mmm) cc_final: 0.8369 (mmt) outliers start: 6 outliers final: 2 residues processed: 226 average time/residue: 0.1066 time to fit residues: 34.8918 Evaluate side-chains 172 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 170 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain B residue 536 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4036 r_free = 0.4036 target = 0.183593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.144571 restraints weight = 14125.032| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.02 r_work: 0.3227 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12660 Z= 0.164 Angle : 0.612 6.916 17142 Z= 0.333 Chirality : 0.042 0.148 1854 Planarity : 0.006 0.064 2120 Dihedral : 7.154 59.933 1678 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.80 % Allowed : 10.70 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.20), residues: 1442 helix: 0.05 (0.15), residues: 918 sheet: -1.69 (0.54), residues: 72 loop : -1.91 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 116 TYR 0.022 0.002 TYR A 406 PHE 0.016 0.001 PHE B 556 TRP 0.017 0.001 TRP A 273 HIS 0.009 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (12652) covalent geometry : angle 0.61041 / 0.33 (17126) SS BOND : bond 0.01003 / 0.72 ( 8) SS BOND : angle 1.34458 / 0.80 ( 16) hydrogen bonds : bond 0.05415 / 3.54 ( 736) hydrogen bonds : angle 5.04231 / 3.49 ( 2160) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 138 TYR cc_start: 0.7625 (m-80) cc_final: 0.7126 (m-80) REVERT: A 215 PHE cc_start: 0.8499 (t80) cc_final: 0.8260 (t80) REVERT: A 221 LYS cc_start: 0.6849 (mtmt) cc_final: 0.6335 (pttm) REVERT: A 360 ARG cc_start: 0.8107 (mtt-85) cc_final: 0.7698 (mtt90) REVERT: A 619 TRP cc_start: 0.7654 (t60) cc_final: 0.7182 (t-100) REVERT: B 138 TYR cc_start: 0.7458 (m-80) cc_final: 0.7139 (m-80) REVERT: B 221 LYS cc_start: 0.6948 (mtmt) cc_final: 0.6122 (pttm) REVERT: B 270 TYR cc_start: 0.8855 (t80) cc_final: 0.8618 (t80) REVERT: B 360 ARG cc_start: 0.8090 (mtt-85) cc_final: 0.7858 (mtt90) REVERT: B 407 GLU cc_start: 0.8072 (tt0) cc_final: 0.7500 (mt-10) REVERT: B 594 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7328 (mt-10) REVERT: B 619 TRP cc_start: 0.7724 (t60) cc_final: 0.7325 (t-100) REVERT: B 652 GLN cc_start: 0.8603 (mt0) cc_final: 0.8386 (mt0) REVERT: B 760 PHE cc_start: 0.8473 (m-80) cc_final: 0.8115 (m-80) REVERT: B 773 MET cc_start: 0.8872 (mmm) cc_final: 0.8282 (mmt) outliers start: 24 outliers final: 12 residues processed: 191 average time/residue: 0.1048 time to fit residues: 29.4382 Evaluate side-chains 165 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 650 TRP Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 650 TRP Chi-restraints excluded: chain B residue 769 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 72 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 chunk 34 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.177565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.139012 restraints weight = 14190.995| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.40 r_work: 0.3145 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12660 Z= 0.206 Angle : 0.619 7.476 17142 Z= 0.334 Chirality : 0.042 0.137 1854 Planarity : 0.006 0.055 2120 Dihedral : 6.820 59.068 1676 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.47 % Allowed : 13.55 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.21), residues: 1442 helix: 0.63 (0.16), residues: 916 sheet: -1.15 (0.63), residues: 52 loop : -1.71 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 542 TYR 0.019 0.002 TYR B 406 PHE 0.021 0.002 PHE B 685 TRP 0.015 0.001 TRP B 397 HIS 0.005 0.001 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 (12652) covalent geometry : angle 0.61894 / 0.33 (17126) SS BOND : bond 0.00259 / 0.14 ( 8) SS BOND : angle 0.89008 / 0.51 ( 16) hydrogen bonds : bond 0.05314 / 3.48 ( 736) hydrogen bonds : angle 4.92157 / 3.42 ( 2160) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 ASN cc_start: 0.8330 (OUTLIER) cc_final: 0.7986 (t0) REVERT: A 138 TYR cc_start: 0.7643 (m-80) cc_final: 0.7204 (m-80) REVERT: A 215 PHE cc_start: 0.8393 (t80) cc_final: 0.8142 (t80) REVERT: A 221 LYS cc_start: 0.6865 (mtmt) cc_final: 0.6156 (pttm) REVERT: A 235 ARG cc_start: 0.7557 (ttt180) cc_final: 0.7269 (mtp180) REVERT: A 346 ILE cc_start: 0.8689 (mm) cc_final: 0.8348 (mt) REVERT: A 360 ARG cc_start: 0.7907 (mtt-85) cc_final: 0.7473 (mtt90) REVERT: A 619 TRP cc_start: 0.7475 (t60) cc_final: 0.6990 (t-100) REVERT: B 138 TYR cc_start: 0.7452 (m-80) cc_final: 0.7054 (m-80) REVERT: B 221 LYS cc_start: 0.6768 (mtmt) cc_final: 0.6259 (pttm) REVERT: B 360 ARG cc_start: 0.7976 (mtt-85) cc_final: 0.7730 (mtt90) REVERT: B 406 TYR cc_start: 0.7980 (t80) cc_final: 0.7655 (t80) REVERT: B 407 GLU cc_start: 0.7890 (tt0) cc_final: 0.7266 (mt-10) REVERT: B 594 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7203 (mt-10) REVERT: B 619 TRP cc_start: 0.7580 (t60) cc_final: 0.7223 (t-100) REVERT: B 652 GLN cc_start: 0.8534 (mt0) cc_final: 0.8262 (mt0) REVERT: B 760 PHE cc_start: 0.8378 (m-80) cc_final: 0.8063 (m-80) outliers start: 33 outliers final: 27 residues processed: 190 average time/residue: 0.0965 time to fit residues: 27.4920 Evaluate side-chains 183 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain 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 365 CYS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 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 780 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 145 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 652 GLN A 655 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.180973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.141522 restraints weight = 14088.866| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.65 r_work: 0.3196 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12660 Z= 0.156 Angle : 0.562 6.415 17142 Z= 0.303 Chirality : 0.041 0.134 1854 Planarity : 0.005 0.053 2120 Dihedral : 6.696 57.870 1676 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.40 % Allowed : 15.87 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.21), residues: 1442 helix: 1.01 (0.16), residues: 916 sheet: -0.78 (0.66), residues: 52 loop : -1.59 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 48 TYR 0.016 0.001 TYR B 406 PHE 0.014 0.001 PHE A 556 TRP 0.015 0.001 TRP B 397 HIS 0.005 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (12652) covalent geometry : angle 0.56150 / 0.30 (17126) SS BOND : bond 0.00167 / 0.08 ( 8) SS BOND : angle 1.17245 / 0.65 ( 16) hydrogen bonds : bond 0.04843 / 3.15 ( 736) hydrogen bonds : angle 4.81781 / 3.36 ( 2160) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.8104 (t0) REVERT: A 138 TYR cc_start: 0.7626 (m-80) cc_final: 0.7152 (m-80) REVERT: A 215 PHE cc_start: 0.8468 (t80) cc_final: 0.8204 (t80) REVERT: A 221 LYS cc_start: 0.7072 (mtmt) cc_final: 0.6388 (pttm) REVERT: A 235 ARG cc_start: 0.7706 (ttt180) cc_final: 0.7358 (mtp180) REVERT: A 481 VAL cc_start: 0.6279 (OUTLIER) cc_final: 0.6058 (p) REVERT: A 619 TRP cc_start: 0.7555 (t60) cc_final: 0.7071 (t-100) REVERT: B 138 TYR cc_start: 0.7464 (m-80) cc_final: 0.7065 (m-80) REVERT: B 221 LYS cc_start: 0.6846 (mtmt) cc_final: 0.6441 (pttm) REVERT: B 406 TYR cc_start: 0.8027 (t80) cc_final: 0.7772 (t80) REVERT: B 407 GLU cc_start: 0.7940 (tt0) cc_final: 0.7387 (mt-10) REVERT: B 481 VAL cc_start: 0.6595 (OUTLIER) cc_final: 0.6393 (p) REVERT: B 619 TRP cc_start: 0.7673 (t60) cc_final: 0.7332 (t-100) REVERT: B 652 GLN cc_start: 0.8529 (mt0) cc_final: 0.8258 (mt0) REVERT: B 659 MET cc_start: 0.8384 (mtp) cc_final: 0.8013 (ttm) REVERT: B 760 PHE cc_start: 0.8531 (m-80) cc_final: 0.8260 (m-80) outliers start: 32 outliers final: 26 residues processed: 183 average time/residue: 0.1060 time to fit residues: 28.9177 Evaluate side-chains 178 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 365 CYS Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 134 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 145 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.180204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.141849 restraints weight = 14120.386| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.47 r_work: 0.3229 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12660 Z= 0.188 Angle : 0.586 6.458 17142 Z= 0.314 Chirality : 0.042 0.136 1854 Planarity : 0.005 0.051 2120 Dihedral : 6.640 59.131 1676 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.29 % Allowed : 15.57 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.22), residues: 1442 helix: 1.14 (0.16), residues: 904 sheet: 0.00 (0.71), residues: 42 loop : -1.54 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 753 TYR 0.016 0.002 TYR A 580 PHE 0.018 0.002 PHE A 685 TRP 0.014 0.001 TRP B 397 HIS 0.003 0.001 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (12652) covalent geometry : angle 0.58496 / 0.31 (17126) SS BOND : bond 0.00359 / 0.20 ( 8) SS BOND : angle 1.14016 / 0.61 ( 16) hydrogen bonds : bond 0.04919 / 3.22 ( 736) hydrogen bonds : angle 4.81682 / 3.36 ( 2160) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 160 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 104 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.8127 (t0) REVERT: A 122 LYS cc_start: 0.7372 (ptpt) cc_final: 0.7066 (pttt) REVERT: A 215 PHE cc_start: 0.8483 (t80) cc_final: 0.8238 (t80) REVERT: A 221 LYS cc_start: 0.6962 (mtmt) cc_final: 0.6273 (pttm) REVERT: A 235 ARG cc_start: 0.7779 (ttt180) cc_final: 0.7415 (mtp180) REVERT: A 346 ILE cc_start: 0.8685 (mm) cc_final: 0.8331 (mt) REVERT: A 619 TRP cc_start: 0.7619 (t60) cc_final: 0.7149 (t-100) REVERT: A 749 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7790 (t70) REVERT: B 96 ARG cc_start: 0.7148 (mtp-110) cc_final: 0.6889 (mtp-110) REVERT: B 138 TYR cc_start: 0.7528 (m-80) cc_final: 0.7133 (m-80) REVERT: B 221 LYS cc_start: 0.6842 (mtmt) cc_final: 0.6474 (pttm) REVERT: B 346 ILE cc_start: 0.8647 (mm) cc_final: 0.8337 (mt) REVERT: B 619 TRP cc_start: 0.7732 (t60) cc_final: 0.7360 (t-100) REVERT: B 652 GLN cc_start: 0.8613 (mt0) cc_final: 0.8357 (mt0) REVERT: B 749 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7813 (t70) REVERT: B 760 PHE cc_start: 0.8467 (m-80) cc_final: 0.8193 (m-80) outliers start: 44 outliers final: 30 residues processed: 195 average time/residue: 0.0927 time to fit residues: 27.4386 Evaluate side-chains 187 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 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 73 PHE Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 73 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 125 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 16 optimal weight: 8.9990 chunk 108 optimal weight: 20.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.180888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.141714 restraints weight = 14100.821| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.32 r_work: 0.3168 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12660 Z= 0.141 Angle : 0.550 7.113 17142 Z= 0.296 Chirality : 0.040 0.152 1854 Planarity : 0.005 0.050 2120 Dihedral : 6.544 58.306 1676 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.07 % Allowed : 16.02 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.22), residues: 1442 helix: 1.29 (0.17), residues: 904 sheet: 0.14 (0.71), residues: 42 loop : -1.47 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 48 TYR 0.065 0.002 TYR B 528 PHE 0.014 0.001 PHE B 556 TRP 0.015 0.001 TRP B 397 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (12652) covalent geometry : angle 0.54794 / 0.30 (17126) SS BOND : bond 0.00267 / 0.16 ( 8) SS BOND : angle 1.79988 / 1.33 ( 16) hydrogen bonds : bond 0.04636 / 3.02 ( 736) hydrogen bonds : angle 4.75322 / 3.32 ( 2160) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8192 (t0) REVERT: A 122 LYS cc_start: 0.7312 (ptpt) cc_final: 0.6989 (pttt) REVERT: A 142 MET cc_start: 0.7108 (ptt) cc_final: 0.6588 (ptt) REVERT: A 221 LYS cc_start: 0.6828 (mtmt) cc_final: 0.6191 (pttm) REVERT: A 619 TRP cc_start: 0.7561 (t60) cc_final: 0.7211 (t-100) REVERT: A 749 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7704 (t70) REVERT: B 96 ARG cc_start: 0.7105 (mtp-110) cc_final: 0.6899 (mtp-110) REVERT: B 221 LYS cc_start: 0.6728 (mtmt) cc_final: 0.6488 (pttm) REVERT: B 517 SER cc_start: 0.8866 (p) cc_final: 0.8505 (p) REVERT: B 619 TRP cc_start: 0.7650 (t60) cc_final: 0.7244 (t-100) REVERT: B 652 GLN cc_start: 0.8481 (mt0) cc_final: 0.8199 (mt0) REVERT: B 749 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7685 (t70) REVERT: B 760 PHE cc_start: 0.8495 (m-80) cc_final: 0.8255 (m-80) outliers start: 41 outliers final: 29 residues processed: 195 average time/residue: 0.0994 time to fit residues: 28.7776 Evaluate side-chains 186 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 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 566 SER Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 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 14 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 11 optimal weight: 0.0020 chunk 103 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 559 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.183513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.143359 restraints weight = 14156.032| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.55 r_work: 0.3252 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12660 Z= 0.124 Angle : 0.539 7.656 17142 Z= 0.290 Chirality : 0.039 0.135 1854 Planarity : 0.005 0.049 2120 Dihedral : 6.328 59.774 1676 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.54 % Allowed : 16.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.22), residues: 1442 helix: 1.41 (0.16), residues: 916 sheet: 0.10 (0.69), residues: 42 loop : -1.43 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 48 TYR 0.045 0.001 TYR A 528 PHE 0.016 0.001 PHE A 558 TRP 0.014 0.001 TRP B 397 HIS 0.002 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (12652) covalent geometry : angle 0.53727 / 0.29 (17126) SS BOND : bond 0.00331 / 0.18 ( 8) SS BOND : angle 1.33265 / 0.97 ( 16) hydrogen bonds : bond 0.04395 / 2.86 ( 736) hydrogen bonds : angle 4.64360 / 3.25 ( 2160) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 ARG cc_start: 0.7875 (ttp-110) cc_final: 0.7620 (ttp-110) REVERT: A 104 ASN cc_start: 0.8421 (OUTLIER) cc_final: 0.8171 (t0) REVERT: A 122 LYS cc_start: 0.7352 (ptpt) cc_final: 0.6974 (pttt) REVERT: A 142 MET cc_start: 0.7059 (ptt) cc_final: 0.6635 (ptt) REVERT: A 221 LYS cc_start: 0.6858 (mtmt) cc_final: 0.6221 (pttm) REVERT: A 268 LEU cc_start: 0.8752 (tt) cc_final: 0.8467 (pp) REVERT: A 517 SER cc_start: 0.8957 (p) cc_final: 0.8598 (p) REVERT: A 619 TRP cc_start: 0.7573 (t60) cc_final: 0.7253 (t-100) REVERT: B 98 ARG cc_start: 0.7786 (ttp-110) cc_final: 0.7220 (ttp-110) REVERT: B 221 LYS cc_start: 0.6811 (mtmt) cc_final: 0.6446 (pttm) REVERT: B 517 SER cc_start: 0.8885 (p) cc_final: 0.8535 (p) REVERT: B 619 TRP cc_start: 0.7611 (t60) cc_final: 0.7293 (t-100) REVERT: B 749 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7777 (t70) REVERT: B 760 PHE cc_start: 0.8450 (m-80) cc_final: 0.8228 (m-80) REVERT: B 851 PHE cc_start: 0.8411 (m-80) cc_final: 0.7999 (m-80) outliers start: 34 outliers final: 22 residues processed: 189 average time/residue: 0.1071 time to fit residues: 30.2440 Evaluate side-chains 184 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 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 721 ASP Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 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 566 SER Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 97 optimal weight: 9.9990 chunk 117 optimal weight: 0.6980 chunk 8 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 125 optimal weight: 0.0030 chunk 55 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 13 optimal weight: 0.0980 chunk 80 optimal weight: 7.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 844 HIS ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.185039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.145743 restraints weight = 14020.804| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.28 r_work: 0.3323 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 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 : 0.002 0.067 12660 Z= 0.116 Angle : 0.526 8.345 17142 Z= 0.283 Chirality : 0.039 0.128 1854 Planarity : 0.005 0.050 2120 Dihedral : 6.159 58.806 1676 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.25 % Allowed : 17.59 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.22), residues: 1442 helix: 1.55 (0.16), residues: 916 sheet: 0.11 (0.70), residues: 42 loop : -1.34 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.057 0.001 TYR B 528 PHE 0.013 0.001 PHE A 556 TRP 0.013 0.001 TRP A 273 HIS 0.002 0.000 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (12652) covalent geometry : angle 0.52530 / 0.28 (17126) SS BOND : bond 0.00192 / 0.12 ( 8) SS BOND : angle 1.22212 / 0.83 ( 16) hydrogen bonds : bond 0.04219 / 2.73 ( 736) hydrogen bonds : angle 4.57393 / 3.20 ( 2160) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7170 (ttm-80) cc_final: 0.6890 (mtp-110) REVERT: A 98 ARG cc_start: 0.7915 (ttp-110) cc_final: 0.7645 (ttp-110) REVERT: A 104 ASN cc_start: 0.8353 (m-40) cc_final: 0.8070 (t0) REVERT: A 122 LYS cc_start: 0.7469 (ptpt) cc_final: 0.7049 (pttt) REVERT: A 142 MET cc_start: 0.7051 (ptt) cc_final: 0.6489 (ptt) REVERT: A 221 LYS cc_start: 0.6859 (mtmt) cc_final: 0.6211 (pttm) REVERT: A 268 LEU cc_start: 0.8688 (tt) cc_final: 0.8465 (pp) REVERT: A 517 SER cc_start: 0.9017 (p) cc_final: 0.8677 (p) REVERT: A 554 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7637 (ttpp) REVERT: A 619 TRP cc_start: 0.7582 (t60) cc_final: 0.7326 (t-100) REVERT: B 98 ARG cc_start: 0.7794 (ttp-110) cc_final: 0.7229 (ttp-110) REVERT: B 221 LYS cc_start: 0.6747 (mtmt) cc_final: 0.6430 (pttm) REVERT: B 517 SER cc_start: 0.8994 (p) cc_final: 0.8680 (p) REVERT: B 619 TRP cc_start: 0.7605 (t60) cc_final: 0.7330 (t-100) REVERT: B 749 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7673 (t70) REVERT: B 851 PHE cc_start: 0.8353 (m-80) cc_final: 0.8098 (m-80) outliers start: 30 outliers final: 21 residues processed: 188 average time/residue: 0.1021 time to fit residues: 28.5675 Evaluate side-chains 182 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 196 TYR 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 550 SER 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 860 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 11 optimal weight: 8.9990 chunk 121 optimal weight: 0.7980 chunk 83 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 70 optimal weight: 0.2980 chunk 126 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.179339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.140109 restraints weight = 14093.562| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.36 r_work: 0.3221 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2583 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 : 0.604 6.497 17142 Z= 0.323 Chirality : 0.042 0.138 1854 Planarity : 0.005 0.051 2120 Dihedral : 6.392 59.378 1676 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.84 % Allowed : 17.14 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.22), residues: 1442 helix: 1.42 (0.17), residues: 904 sheet: 0.12 (0.69), residues: 42 loop : -1.37 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 753 TYR 0.078 0.002 TYR B 528 PHE 0.021 0.002 PHE B 760 TRP 0.017 0.001 TRP B 829 HIS 0.004 0.001 HIS B 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 (12652) covalent geometry : angle 0.60226 / 0.32 (17126) SS BOND : bond 0.00287 / 0.15 ( 8) SS BOND : angle 1.58419 / 1.04 ( 16) hydrogen bonds : bond 0.04846 / 3.16 ( 736) hydrogen bonds : angle 4.70195 / 3.28 ( 2160) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASN cc_start: 0.8427 (OUTLIER) cc_final: 0.8220 (t0) REVERT: A 122 LYS cc_start: 0.7464 (ptpt) cc_final: 0.7086 (pttt) REVERT: A 142 MET cc_start: 0.7279 (ptt) cc_final: 0.6704 (ptt) REVERT: A 221 LYS cc_start: 0.6782 (mtmt) cc_final: 0.6324 (pttm) REVERT: A 554 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7526 (ttpp) REVERT: A 619 TRP cc_start: 0.7564 (t60) cc_final: 0.7199 (t-100) REVERT: B 517 SER cc_start: 0.8912 (p) cc_final: 0.8551 (p) REVERT: B 619 TRP cc_start: 0.7625 (t60) cc_final: 0.7260 (t-100) REVERT: B 749 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7769 (t0) REVERT: B 851 PHE cc_start: 0.8421 (m-80) cc_final: 0.8179 (m-80) outliers start: 38 outliers final: 29 residues processed: 185 average time/residue: 0.0972 time to fit residues: 27.0004 Evaluate side-chains 189 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 507 MET Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 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 536 THR Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 566 SER 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 33 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 140 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.180128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.131889 restraints weight = 14169.557| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.84 r_work: 0.3233 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12660 Z= 0.173 Angle : 0.585 7.771 17142 Z= 0.313 Chirality : 0.041 0.138 1854 Planarity : 0.005 0.051 2120 Dihedral : 6.404 59.945 1676 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.69 % Allowed : 17.22 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.22), residues: 1442 helix: 1.40 (0.17), residues: 904 sheet: 0.06 (0.69), residues: 42 loop : -1.40 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 98 TYR 0.027 0.002 TYR B 406 PHE 0.024 0.002 PHE B 760 TRP 0.013 0.001 TRP B 829 HIS 0.003 0.001 HIS B 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (12652) covalent geometry : angle 0.58363 / 0.31 (17126) SS BOND : bond 0.00280 / 0.16 ( 8) SS BOND : angle 1.46534 / 0.97 ( 16) hydrogen bonds : bond 0.04711 / 3.07 ( 736) hydrogen bonds : angle 4.70889 / 3.29 ( 2160) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7252 (ttm-80) cc_final: 0.6966 (mtp-110) REVERT: A 122 LYS cc_start: 0.7487 (ptpt) cc_final: 0.7117 (pttt) REVERT: A 142 MET cc_start: 0.7322 (ptt) cc_final: 0.6798 (ptt) REVERT: A 221 LYS cc_start: 0.6893 (mtmt) cc_final: 0.6402 (pttm) REVERT: A 554 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7629 (ttpp) REVERT: A 619 TRP cc_start: 0.7705 (t60) cc_final: 0.7331 (t-100) REVERT: B 517 SER cc_start: 0.8946 (p) cc_final: 0.8589 (p) REVERT: B 619 TRP cc_start: 0.7702 (t60) cc_final: 0.7333 (t-100) REVERT: B 749 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7923 (t70) REVERT: B 851 PHE cc_start: 0.8546 (m-80) cc_final: 0.8284 (m-80) outliers start: 36 outliers final: 30 residues processed: 186 average time/residue: 0.1013 time to fit residues: 28.2152 Evaluate side-chains 190 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 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 769 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 566 SER 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 109 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 2 optimal weight: 4.9990 chunk 34 optimal weight: 20.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.183064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.138590 restraints weight = 14047.634| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.95 r_work: 0.3312 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12660 Z= 0.129 Angle : 0.558 8.019 17142 Z= 0.297 Chirality : 0.040 0.134 1854 Planarity : 0.005 0.052 2120 Dihedral : 6.301 59.948 1676 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.25 % Allowed : 17.89 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.22), residues: 1442 helix: 1.51 (0.17), residues: 904 sheet: 0.01 (0.68), residues: 42 loop : -1.35 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 98 TYR 0.024 0.001 TYR B 406 PHE 0.022 0.001 PHE B 760 TRP 0.014 0.001 TRP A 397 HIS 0.002 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (12652) covalent geometry : angle 0.55689 / 0.30 (17126) SS BOND : bond 0.00220 / 0.12 ( 8) SS BOND : angle 1.27799 / 0.85 ( 16) hydrogen bonds : bond 0.04417 / 2.87 ( 736) hydrogen bonds : angle 4.64097 / 3.24 ( 2160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2716.44 seconds wall clock time: 47 minutes 25.14 seconds (2845.14 seconds total)