Starting phenix.real_space_refine on Sat Jul 4 04:12:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l2x_23144/07_2026/7l2x_23144.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l2x_23144/07_2026/7l2x_23144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l2x_23144/07_2026/7l2x_23144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l2x_23144/07_2026/7l2x_23144.map" model { file = "/net/cci-nas-00/data/ceres_data/7l2x_23144/07_2026/7l2x_23144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l2x_23144/07_2026/7l2x_23144.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7l2x_23144/07_2026/7l2x_23144.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l2x_23144/07_2026/7l2x_23144.cif" } resolution = 3.26 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= 0.002 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 100 5.16 5 C 11655 2.51 5 N 2817 2.21 5 O 3169 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17745 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4349 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "D" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4349 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "B" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4349 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "C" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4349 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "A" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 122 Unusual residues: {'6EU': 1, '6IY': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 97 Unusual residues: {'6EU': 1, '6IY': 1, 'XPJ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'6EU': 1, '6IY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.91, per 1000 atoms: 0.16 Number of scatterers: 17745 At special positions: 0 Unit cell: (126.92, 127.755, 110.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 4 15.00 O 3169 8.00 N 2817 7.00 C 11655 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 702.4 milliseconds 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4056 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 4 sheets defined 63.5% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 213 through 223 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 345 through 354 removed outlier: 3.535A pdb=" N GLN A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 411 through 414 Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.521A pdb=" N PHE A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 454 removed outlier: 3.634A pdb=" N ILE A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 510 through 532 Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.692A pdb=" N SER A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 557 Processing helix chain 'A' and resid 562 through 575 removed outlier: 4.259A pdb=" N ALA A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 599 removed outlier: 4.307A pdb=" N PHE A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 642 Processing helix chain 'A' and resid 655 through 671 Processing helix chain 'A' and resid 673 through 689 removed outlier: 3.650A pdb=" N ILE A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 712 removed outlier: 3.590A pdb=" N LYS A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 699 " --> pdb=" O ASN A 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 211 Processing helix chain 'D' and resid 213 through 223 Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 260 through 270 Processing helix chain 'D' and resid 286 through 294 Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 324 through 328 removed outlier: 3.560A pdb=" N GLU D 327 " --> pdb=" O LYS D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 354 Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 410 through 414 Processing helix chain 'D' and resid 415 through 429 Processing helix chain 'D' and resid 429 through 454 removed outlier: 3.599A pdb=" N ILE D 433 " --> pdb=" O PHE D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 510 through 532 Processing helix chain 'D' and resid 536 through 551 Processing helix chain 'D' and resid 552 through 557 Processing helix chain 'D' and resid 562 through 575 removed outlier: 4.243A pdb=" N ALA D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 599 removed outlier: 4.544A pdb=" N PHE D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 642 Processing helix chain 'D' and resid 655 through 671 Processing helix chain 'D' and resid 672 through 690 removed outlier: 3.832A pdb=" N ASN D 676 " --> pdb=" O ILE D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 711 removed outlier: 3.531A pdb=" N LYS D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER D 711 " --> pdb=" O ASP D 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 211 Processing helix chain 'B' and resid 213 through 223 Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.598A pdb=" N LYS B 237 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 270 removed outlier: 3.522A pdb=" N VAL B 264 " --> pdb=" O GLN B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 294 Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 324 through 328 removed outlier: 3.599A pdb=" N GLU B 327 " --> pdb=" O LYS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 345 through 354 Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 410 through 414 Processing helix chain 'B' and resid 415 through 429 removed outlier: 3.598A pdb=" N PHE B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 454 Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 510 through 532 Processing helix chain 'B' and resid 536 through 551 removed outlier: 4.069A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 557 Processing helix chain 'B' and resid 563 through 575 removed outlier: 3.676A pdb=" N VAL B 567 " --> pdb=" O GLY B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 599 removed outlier: 4.488A pdb=" N PHE B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 642 Processing helix chain 'B' and resid 655 through 671 Processing helix chain 'B' and resid 672 through 688 removed outlier: 3.931A pdb=" N ASN B 676 " --> pdb=" O ILE B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 712 Processing helix chain 'C' and resid 203 through 211 Processing helix chain 'C' and resid 213 through 223 Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 260 through 270 Processing helix chain 'C' and resid 286 through 294 Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 362 through 366 Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 410 through 414 Processing helix chain 'C' and resid 415 through 429 removed outlier: 3.519A pdb=" N PHE C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 454 removed outlier: 3.631A pdb=" N ILE C 433 " --> pdb=" O PHE C 429 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR C 454 " --> pdb=" O ALA C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 510 through 532 Processing helix chain 'C' and resid 536 through 551 removed outlier: 3.628A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 557 Processing helix chain 'C' and resid 563 through 599 removed outlier: 3.731A pdb=" N VAL C 567 " --> pdb=" O GLY C 563 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 642 Processing helix chain 'C' and resid 655 through 672 Processing helix chain 'C' and resid 673 through 689 Processing helix chain 'C' and resid 692 through 712 removed outlier: 4.336A pdb=" N LYS C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 373 removed outlier: 6.860A pdb=" N SER A 379 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ALA A 373 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 368 through 373 removed outlier: 6.702A pdb=" N SER D 379 " --> pdb=" O GLU D 371 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ALA D 373 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 368 through 373 removed outlier: 5.226A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 369 through 373 removed outlier: 6.826A pdb=" N SER C 379 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ALA C 373 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2883 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: 2.21 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2722 1.30 - 1.43: 5097 1.43 - 1.55: 10189 1.55 - 1.68: 8 1.68 - 1.81: 164 Bond restraints: 18180 Sorted by residual: bond pdb=" CBK 6EU B 901 " pdb=" OAF 6EU B 901 " ideal model delta sigma weight residual 1.329 1.453 -0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" CBK 6EU D 901 " pdb=" OAF 6EU D 901 " ideal model delta sigma weight residual 1.329 1.453 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" CBK 6EU A 901 " pdb=" OAF 6EU A 901 " ideal model delta sigma weight residual 1.329 1.453 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" CBK 6EU C 901 " pdb=" OAF 6EU C 901 " ideal model delta sigma weight residual 1.329 1.453 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" C13 6IY B 902 " pdb=" O6 6IY B 902 " ideal model delta sigma weight residual 1.333 1.418 -0.085 2.00e-02 2.50e+03 1.81e+01 ... (remaining 18175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.75: 24470 4.75 - 9.51: 143 9.51 - 14.26: 14 14.26 - 19.01: 0 19.01 - 23.77: 4 Bond angle restraints: 24631 Sorted by residual: angle pdb=" O3 6IY B 902 " pdb=" P 6IY B 902 " pdb=" O4 6IY B 902 " ideal model delta sigma weight residual 123.06 99.29 23.77 3.00e+00 1.11e-01 6.28e+01 angle pdb=" O3 6IY A 903 " pdb=" P 6IY A 903 " pdb=" O4 6IY A 903 " ideal model delta sigma weight residual 123.06 100.73 22.33 3.00e+00 1.11e-01 5.54e+01 angle pdb=" O3 6IY D 902 " pdb=" P 6IY D 902 " pdb=" O4 6IY D 902 " ideal model delta sigma weight residual 123.06 100.88 22.18 3.00e+00 1.11e-01 5.46e+01 angle pdb=" O3 6IY A 902 " pdb=" P 6IY A 902 " pdb=" O4 6IY A 902 " ideal model delta sigma weight residual 123.06 102.23 20.83 3.00e+00 1.11e-01 4.82e+01 angle pdb=" C SER A 711 " pdb=" N PHE A 712 " pdb=" CA PHE A 712 " ideal model delta sigma weight residual 121.54 130.89 -9.35 1.91e+00 2.74e-01 2.40e+01 ... (remaining 24626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.45: 10167 21.45 - 42.90: 381 42.90 - 64.35: 68 64.35 - 85.80: 36 85.80 - 107.26: 13 Dihedral angle restraints: 10665 sinusoidal: 4345 harmonic: 6320 Sorted by residual: dihedral pdb=" CA VAL B 415 " pdb=" C VAL B 415 " pdb=" N GLU B 416 " pdb=" CA GLU B 416 " ideal model delta harmonic sigma weight residual -180.00 -153.73 -26.27 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA VAL D 415 " pdb=" C VAL D 415 " pdb=" N GLU D 416 " pdb=" CA GLU D 416 " ideal model delta harmonic sigma weight residual -180.00 -155.61 -24.39 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA GLN D 561 " pdb=" C GLN D 561 " pdb=" N MET D 562 " pdb=" CA MET D 562 " ideal model delta harmonic sigma weight residual -180.00 -156.85 -23.15 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 10662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2541 0.087 - 0.173: 207 0.173 - 0.260: 2 0.260 - 0.346: 1 0.346 - 0.433: 5 Chirality restraints: 2756 Sorted by residual: chirality pdb=" CAO 6EU B 901 " pdb=" CAJ 6EU B 901 " pdb=" CAR 6EU B 901 " pdb=" CAW 6EU B 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.67 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CAO 6EU A 901 " pdb=" CAJ 6EU A 901 " pdb=" CAR 6EU A 901 " pdb=" CAW 6EU A 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.67 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CAO 6EU C 901 " pdb=" CAJ 6EU C 901 " pdb=" CAR 6EU C 901 " pdb=" CAW 6EU C 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.67 0.43 2.00e-01 2.50e+01 4.64e+00 ... (remaining 2753 not shown) Planarity restraints: 3020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 539 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.02e+00 pdb=" C ALA D 539 " -0.052 2.00e-02 2.50e+03 pdb=" O ALA D 539 " 0.019 2.00e-02 2.50e+03 pdb=" N SER D 540 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 569 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.01e+00 pdb=" C ILE B 569 " -0.052 2.00e-02 2.50e+03 pdb=" O ILE B 569 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU B 570 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 541 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.07e+00 pdb=" C MET A 541 " -0.049 2.00e-02 2.50e+03 pdb=" O MET A 541 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 542 " 0.017 2.00e-02 2.50e+03 ... (remaining 3017 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1345 2.72 - 3.27: 18126 3.27 - 3.81: 28164 3.81 - 4.36: 34050 4.36 - 4.90: 59353 Nonbonded interactions: 141038 Sorted by model distance: nonbonded pdb=" OG1 THR B 731 " pdb=" OD1 ASP B 733 " model vdw 2.179 3.040 nonbonded pdb=" OG1 THR C 731 " pdb=" OD1 ASP C 733 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR D 731 " pdb=" OD1 ASP D 733 " model vdw 2.233 3.040 nonbonded pdb=" O ALA C 719 " pdb=" NH1 ARG C 721 " model vdw 2.247 3.120 nonbonded pdb=" NH2 ARG C 557 " pdb=" OE1 GLU C 570 " model vdw 2.257 3.120 ... (remaining 141033 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 193 through 901) selection = (chain 'B' and resid 193 through 901) selection = chain 'C' selection = (chain 'D' and resid 193 through 901) } 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: 2.480 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: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 13.020 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 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 0.124 18180 Z= 0.473 Angle : 1.058 23.766 24631 Z= 0.524 Chirality : 0.053 0.433 2756 Planarity : 0.006 0.042 3020 Dihedral : 13.558 107.256 6609 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.01 % Favored : 94.94 % Rotamer: Outliers : 0.79 % Allowed : 1.58 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.61 (0.18), residues: 2136 helix: 1.51 (0.13), residues: 1248 sheet: -0.77 (0.55), residues: 76 loop : -1.25 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 455 TYR 0.030 0.003 TYR D 627 PHE 0.039 0.003 PHE B 304 TRP 0.016 0.002 TRP D 372 HIS 0.008 0.002 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.01047 / 0.47 (18180) covalent geometry : angle 1.05816 / 0.52 (24631) hydrogen bonds : bond 0.14725 / 9.97 ( 996) hydrogen bonds : angle 5.22942 / 3.77 ( 2883) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 619 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 GLN cc_start: 0.8809 (tp40) cc_final: 0.8466 (tp-100) REVERT: A 504 LYS cc_start: 0.8839 (mttt) cc_final: 0.8632 (mttm) REVERT: A 557 ARG cc_start: 0.8923 (mtt180) cc_final: 0.8618 (mtt-85) REVERT: A 636 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7309 (tp30) REVERT: D 368 LYS cc_start: 0.8286 (tttt) cc_final: 0.7759 (tttp) REVERT: D 374 TYR cc_start: 0.6458 (m-80) cc_final: 0.5886 (m-10) REVERT: D 378 HIS cc_start: 0.7501 (p-80) cc_final: 0.6941 (p90) REVERT: D 410 HIS cc_start: 0.8477 (p-80) cc_final: 0.8209 (p90) REVERT: D 423 GLN cc_start: 0.8717 (tp40) cc_final: 0.8480 (tp-100) REVERT: D 571 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8192 (tptp) REVERT: D 581 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7319 (mmt) REVERT: B 211 ARG cc_start: 0.8199 (mtt180) cc_final: 0.7965 (mmm160) REVERT: B 324 LYS cc_start: 0.8923 (mttt) cc_final: 0.8639 (mptt) REVERT: B 410 HIS cc_start: 0.7874 (m90) cc_final: 0.7639 (m-70) REVERT: B 416 GLU cc_start: 0.7553 (tp30) cc_final: 0.6926 (tp30) REVERT: B 420 ARG cc_start: 0.8478 (mmt180) cc_final: 0.8118 (mmm-85) REVERT: B 423 GLN cc_start: 0.8895 (tp40) cc_final: 0.8496 (tp-100) REVERT: B 703 ILE cc_start: 0.9621 (mt) cc_final: 0.9378 (mp) REVERT: C 343 SER cc_start: 0.9075 (m) cc_final: 0.8785 (p) REVERT: C 483 SER cc_start: 0.9483 (t) cc_final: 0.9278 (p) REVERT: C 636 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7962 (mm-30) outliers start: 15 outliers final: 4 residues processed: 629 average time/residue: 0.1353 time to fit residues: 123.3439 Evaluate side-chains 412 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 407 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain C residue 653 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 378 HIS D 410 HIS ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 GLN B 289 HIS B 378 HIS C 285 ASN C 378 HIS C 393 ASN C 410 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.153826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.103679 restraints weight = 28898.846| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.67 r_work: 0.3032 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18180 Z= 0.136 Angle : 0.588 7.070 24631 Z= 0.311 Chirality : 0.040 0.176 2756 Planarity : 0.004 0.047 3020 Dihedral : 11.125 105.771 2546 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.63 % Favored : 95.27 % Rotamer: Outliers : 1.85 % Allowed : 8.33 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.62 (0.18), residues: 2136 helix: 2.48 (0.14), residues: 1252 sheet: -0.52 (0.54), residues: 76 loop : -1.12 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 575 TYR 0.032 0.001 TYR A 309 PHE 0.051 0.001 PHE D 304 TRP 0.012 0.001 TRP D 426 HIS 0.010 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 (18180) covalent geometry : angle 0.58836 / 0.31 (24631) hydrogen bonds : bond 0.04938 / 3.34 ( 996) hydrogen bonds : angle 3.85510 / 2.78 ( 2883) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 459 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 HIS cc_start: 0.7887 (p-80) cc_final: 0.7660 (p90) REVERT: A 423 GLN cc_start: 0.9026 (tp40) cc_final: 0.8766 (tp-100) REVERT: A 504 LYS cc_start: 0.9080 (mttt) cc_final: 0.8820 (mtpp) REVERT: A 636 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8269 (tp30) REVERT: D 410 HIS cc_start: 0.8258 (p90) cc_final: 0.7800 (p90) REVERT: D 433 ILE cc_start: 0.9360 (mm) cc_final: 0.9148 (mt) REVERT: D 571 LYS cc_start: 0.8690 (mmtt) cc_final: 0.8387 (tptp) REVERT: B 250 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7725 (mt) REVERT: B 324 LYS cc_start: 0.8963 (mttt) cc_final: 0.8516 (mptt) REVERT: B 410 HIS cc_start: 0.7970 (m90) cc_final: 0.7702 (m-70) REVERT: B 416 GLU cc_start: 0.7789 (tp30) cc_final: 0.7253 (tp30) REVERT: B 420 ARG cc_start: 0.8780 (mmt180) cc_final: 0.8431 (mmm-85) REVERT: B 653 TYR cc_start: 0.6502 (OUTLIER) cc_final: 0.5522 (p90) REVERT: B 700 GLN cc_start: 0.8720 (tp40) cc_final: 0.8178 (tp40) REVERT: B 724 LYS cc_start: 0.8807 (tmtt) cc_final: 0.8552 (tmtt) REVERT: C 309 TYR cc_start: 0.8939 (t80) cc_final: 0.8527 (t80) REVERT: C 342 SER cc_start: 0.9163 (t) cc_final: 0.8849 (p) REVERT: C 343 SER cc_start: 0.9008 (m) cc_final: 0.8593 (p) REVERT: C 420 ARG cc_start: 0.8780 (mmm-85) cc_final: 0.8446 (mmm-85) REVERT: C 471 ASP cc_start: 0.8631 (m-30) cc_final: 0.7756 (t0) REVERT: C 648 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7755 (mm-30) REVERT: C 700 GLN cc_start: 0.8944 (tp40) cc_final: 0.8698 (tp40) REVERT: C 716 MET cc_start: 0.4922 (ptm) cc_final: 0.4317 (ptp) REVERT: C 740 TRP cc_start: 0.8617 (m100) cc_final: 0.8229 (m100) REVERT: C 743 ARG cc_start: 0.8533 (ttm-80) cc_final: 0.7722 (tpp80) outliers start: 35 outliers final: 19 residues processed: 476 average time/residue: 0.1154 time to fit residues: 84.4974 Evaluate side-chains 421 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 400 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 466 LYS Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 653 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 23 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 184 optimal weight: 4.9990 chunk 181 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 498 GLN B 273 GLN B 378 HIS C 206 HIS C 393 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.149656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.099438 restraints weight = 29372.520| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.62 r_work: 0.2963 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18180 Z= 0.223 Angle : 0.604 7.178 24631 Z= 0.315 Chirality : 0.041 0.209 2756 Planarity : 0.004 0.056 3020 Dihedral : 10.069 90.703 2539 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.20 % Favored : 94.76 % Rotamer: Outliers : 2.22 % Allowed : 11.23 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.71 (0.19), residues: 2136 helix: 2.58 (0.14), residues: 1272 sheet: -0.46 (0.56), residues: 76 loop : -1.23 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 211 TYR 0.016 0.002 TYR B 584 PHE 0.044 0.002 PHE D 304 TRP 0.011 0.001 TRP D 549 HIS 0.013 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.22 (18180) covalent geometry : angle 0.60433 / 0.32 (24631) hydrogen bonds : bond 0.05371 / 3.61 ( 996) hydrogen bonds : angle 3.97199 / 2.85 ( 2883) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 410 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 HIS cc_start: 0.7898 (p-80) cc_final: 0.7650 (p90) REVERT: A 423 GLN cc_start: 0.9108 (tp40) cc_final: 0.8841 (tp-100) REVERT: A 504 LYS cc_start: 0.9071 (mttt) cc_final: 0.8807 (mtpp) REVERT: A 584 TYR cc_start: 0.8886 (t80) cc_final: 0.8659 (t80) REVERT: A 636 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8337 (tp30) REVERT: A 700 GLN cc_start: 0.9019 (tp-100) cc_final: 0.8702 (tp40) REVERT: D 410 HIS cc_start: 0.8383 (p90) cc_final: 0.7783 (p90) REVERT: D 424 ASP cc_start: 0.9037 (t70) cc_final: 0.8756 (t70) REVERT: D 571 LYS cc_start: 0.8740 (mmtt) cc_final: 0.8408 (tptp) REVERT: D 653 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.5733 (p90) REVERT: B 324 LYS cc_start: 0.8980 (mttt) cc_final: 0.8530 (mptt) REVERT: B 410 HIS cc_start: 0.7955 (m90) cc_final: 0.7728 (m-70) REVERT: B 416 GLU cc_start: 0.7864 (tp30) cc_final: 0.7259 (tp30) REVERT: B 420 ARG cc_start: 0.8843 (mmt180) cc_final: 0.8423 (mmm-85) REVERT: B 653 TYR cc_start: 0.6568 (OUTLIER) cc_final: 0.5777 (p90) REVERT: C 342 SER cc_start: 0.9188 (t) cc_final: 0.8911 (p) REVERT: C 343 SER cc_start: 0.9048 (m) cc_final: 0.8639 (p) REVERT: C 420 ARG cc_start: 0.8782 (mmm-85) cc_final: 0.8447 (mmm-85) REVERT: C 503 LEU cc_start: 0.8848 (mp) cc_final: 0.8631 (mt) REVERT: C 700 GLN cc_start: 0.8930 (tp40) cc_final: 0.8445 (tp-100) REVERT: C 716 MET cc_start: 0.5080 (ptm) cc_final: 0.4242 (ptp) REVERT: C 743 ARG cc_start: 0.8548 (ttm-80) cc_final: 0.7764 (tpp80) outliers start: 42 outliers final: 29 residues processed: 436 average time/residue: 0.1079 time to fit residues: 73.7344 Evaluate side-chains 418 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 387 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 741 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 24 optimal weight: 4.9990 chunk 54 optimal weight: 0.0770 chunk 5 optimal weight: 0.8980 chunk 189 optimal weight: 4.9990 chunk 180 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 51 optimal weight: 0.2980 chunk 28 optimal weight: 7.9990 chunk 151 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 273 GLN C 206 HIS C 393 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.153932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.103631 restraints weight = 29072.098| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.67 r_work: 0.3031 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 18180 Z= 0.110 Angle : 0.538 8.797 24631 Z= 0.279 Chirality : 0.037 0.148 2756 Planarity : 0.003 0.047 3020 Dihedral : 9.358 89.951 2539 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.01 % Favored : 94.94 % Rotamer: Outliers : 1.27 % Allowed : 13.03 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.02 (0.19), residues: 2136 helix: 2.85 (0.14), residues: 1276 sheet: -0.24 (0.58), residues: 76 loop : -1.18 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 331 TYR 0.021 0.001 TYR C 309 PHE 0.045 0.001 PHE D 304 TRP 0.009 0.001 TRP D 549 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (18180) covalent geometry : angle 0.53756 / 0.28 (24631) hydrogen bonds : bond 0.04125 / 2.78 ( 996) hydrogen bonds : angle 3.74181 / 2.69 ( 2883) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 423 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 HIS cc_start: 0.7832 (p-80) cc_final: 0.7596 (p90) REVERT: A 423 GLN cc_start: 0.9050 (tp40) cc_final: 0.8783 (tp-100) REVERT: A 584 TYR cc_start: 0.8723 (t80) cc_final: 0.8422 (t80) REVERT: D 354 GLN cc_start: 0.8727 (mt0) cc_final: 0.8358 (mt0) REVERT: D 410 HIS cc_start: 0.8319 (p90) cc_final: 0.7703 (p90) REVERT: D 424 ASP cc_start: 0.9004 (t70) cc_final: 0.8671 (t70) REVERT: D 433 ILE cc_start: 0.9378 (mm) cc_final: 0.9161 (mt) REVERT: D 571 LYS cc_start: 0.8739 (mmtt) cc_final: 0.8453 (tptp) REVERT: D 653 TYR cc_start: 0.7184 (OUTLIER) cc_final: 0.5639 (p90) REVERT: B 324 LYS cc_start: 0.8951 (mttt) cc_final: 0.8522 (mptt) REVERT: B 354 GLN cc_start: 0.8640 (mt0) cc_final: 0.8341 (mt0) REVERT: B 371 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7793 (tp30) REVERT: B 410 HIS cc_start: 0.7907 (m90) cc_final: 0.7648 (m-70) REVERT: B 483 SER cc_start: 0.9284 (t) cc_final: 0.9035 (p) REVERT: B 653 TYR cc_start: 0.6566 (OUTLIER) cc_final: 0.5641 (p90) REVERT: B 724 LYS cc_start: 0.8722 (tmtt) cc_final: 0.8414 (tmtt) REVERT: C 331 ARG cc_start: 0.8048 (ttm-80) cc_final: 0.7770 (tpp80) REVERT: C 342 SER cc_start: 0.9160 (t) cc_final: 0.8906 (p) REVERT: C 343 SER cc_start: 0.9003 (m) cc_final: 0.8533 (p) REVERT: C 391 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8261 (mm-30) REVERT: C 397 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7961 (mt-10) REVERT: C 420 ARG cc_start: 0.8785 (mmm-85) cc_final: 0.8415 (mmm-85) REVERT: C 653 TYR cc_start: 0.6738 (OUTLIER) cc_final: 0.5319 (p90) REVERT: C 700 GLN cc_start: 0.8987 (tp40) cc_final: 0.8526 (tp-100) REVERT: C 716 MET cc_start: 0.5164 (ptm) cc_final: 0.4359 (ptp) REVERT: C 740 TRP cc_start: 0.8616 (m100) cc_final: 0.8274 (m100) REVERT: C 743 ARG cc_start: 0.8492 (ttm-80) cc_final: 0.7775 (tpp80) outliers start: 24 outliers final: 11 residues processed: 436 average time/residue: 0.1129 time to fit residues: 76.4482 Evaluate side-chains 406 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 392 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 653 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 113 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 165 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 727 GLN B 378 HIS C 206 HIS C 393 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.150866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.099715 restraints weight = 29175.521| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.65 r_work: 0.2974 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 18180 Z= 0.199 Angle : 0.576 7.192 24631 Z= 0.299 Chirality : 0.040 0.178 2756 Planarity : 0.004 0.057 3020 Dihedral : 8.973 88.128 2539 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.06 % Favored : 94.90 % Rotamer: Outliers : 2.06 % Allowed : 13.71 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.90 (0.19), residues: 2136 helix: 2.75 (0.14), residues: 1276 sheet: -0.25 (0.60), residues: 76 loop : -1.23 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 331 TYR 0.019 0.001 TYR C 309 PHE 0.047 0.001 PHE D 304 TRP 0.013 0.001 TRP D 426 HIS 0.011 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (18180) covalent geometry : angle 0.57592 / 0.30 (24631) hydrogen bonds : bond 0.04878 / 3.27 ( 996) hydrogen bonds : angle 3.93518 / 2.83 ( 2883) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 399 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 HIS cc_start: 0.7875 (p-80) cc_final: 0.7602 (p90) REVERT: A 423 GLN cc_start: 0.9093 (tp40) cc_final: 0.8828 (tp-100) REVERT: A 584 TYR cc_start: 0.8886 (t80) cc_final: 0.8625 (t80) REVERT: D 354 GLN cc_start: 0.8752 (mt0) cc_final: 0.8363 (mt0) REVERT: D 410 HIS cc_start: 0.8379 (p90) cc_final: 0.7712 (p90) REVERT: D 424 ASP cc_start: 0.9052 (t70) cc_final: 0.8719 (t70) REVERT: D 571 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8409 (tptp) REVERT: D 653 TYR cc_start: 0.7279 (OUTLIER) cc_final: 0.5802 (p90) REVERT: D 716 MET cc_start: 0.5186 (ppp) cc_final: 0.4842 (ppp) REVERT: B 324 LYS cc_start: 0.8936 (mttt) cc_final: 0.8484 (mptt) REVERT: B 371 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7831 (tp30) REVERT: B 410 HIS cc_start: 0.7918 (m90) cc_final: 0.7695 (m-70) REVERT: B 416 GLU cc_start: 0.7845 (tp30) cc_final: 0.7393 (tp30) REVERT: B 420 ARG cc_start: 0.9002 (mmm-85) cc_final: 0.8434 (mmm-85) REVERT: B 653 TYR cc_start: 0.6633 (OUTLIER) cc_final: 0.5757 (p90) REVERT: B 724 LYS cc_start: 0.8769 (tmtt) cc_final: 0.8461 (tmtt) REVERT: C 342 SER cc_start: 0.9191 (t) cc_final: 0.8930 (p) REVERT: C 343 SER cc_start: 0.9015 (m) cc_final: 0.8550 (p) REVERT: C 351 TYR cc_start: 0.8757 (t80) cc_final: 0.8508 (t80) REVERT: C 420 ARG cc_start: 0.8789 (mmm-85) cc_final: 0.8431 (mmm-85) REVERT: C 504 LYS cc_start: 0.9036 (ttmt) cc_final: 0.8708 (ttmm) REVERT: C 648 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7707 (mm-30) REVERT: C 700 GLN cc_start: 0.8956 (tp40) cc_final: 0.8564 (tp-100) REVERT: C 716 MET cc_start: 0.5135 (ptm) cc_final: 0.4267 (ptp) REVERT: C 740 TRP cc_start: 0.8635 (m100) cc_final: 0.8250 (m100) REVERT: C 743 ARG cc_start: 0.8499 (ttm-80) cc_final: 0.7816 (tpp80) outliers start: 39 outliers final: 28 residues processed: 421 average time/residue: 0.1077 time to fit residues: 70.6397 Evaluate side-chains 415 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 385 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 741 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 191 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 205 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 GLN D 270 ASN B 273 GLN B 378 HIS C 206 HIS C 393 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.152722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.102005 restraints weight = 28862.647| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.65 r_work: 0.3009 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18180 Z= 0.133 Angle : 0.532 7.710 24631 Z= 0.277 Chirality : 0.038 0.161 2756 Planarity : 0.003 0.039 3020 Dihedral : 8.585 85.749 2539 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.95 % Allowed : 14.45 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.03 (0.19), residues: 2136 helix: 2.91 (0.14), residues: 1252 sheet: -0.16 (0.60), residues: 76 loop : -1.16 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 701 TYR 0.018 0.001 TYR C 309 PHE 0.041 0.001 PHE D 304 TRP 0.011 0.001 TRP A 372 HIS 0.014 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (18180) covalent geometry : angle 0.53163 / 0.28 (24631) hydrogen bonds : bond 0.04241 / 2.85 ( 996) hydrogen bonds : angle 3.81885 / 2.75 ( 2883) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 403 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 HIS cc_start: 0.7895 (p-80) cc_final: 0.7602 (p90) REVERT: A 423 GLN cc_start: 0.9081 (tp40) cc_final: 0.8819 (tp-100) REVERT: A 584 TYR cc_start: 0.8802 (t80) cc_final: 0.8516 (t80) REVERT: D 354 GLN cc_start: 0.8741 (mt0) cc_final: 0.8314 (mp10) REVERT: D 410 HIS cc_start: 0.8363 (p90) cc_final: 0.7678 (p90) REVERT: D 424 ASP cc_start: 0.9035 (t70) cc_final: 0.8721 (t70) REVERT: D 571 LYS cc_start: 0.8759 (mmtt) cc_final: 0.8474 (tptp) REVERT: D 653 TYR cc_start: 0.7249 (OUTLIER) cc_final: 0.5778 (p90) REVERT: B 324 LYS cc_start: 0.8883 (mttt) cc_final: 0.8354 (mmtt) REVERT: B 354 GLN cc_start: 0.8599 (mt0) cc_final: 0.8303 (mt0) REVERT: B 371 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7872 (tp30) REVERT: B 410 HIS cc_start: 0.7876 (m90) cc_final: 0.7644 (m-70) REVERT: B 420 ARG cc_start: 0.9022 (mmm-85) cc_final: 0.8808 (mmm-85) REVERT: B 653 TYR cc_start: 0.6647 (OUTLIER) cc_final: 0.5730 (p90) REVERT: C 222 GLU cc_start: 0.8654 (pt0) cc_final: 0.8450 (pt0) REVERT: C 342 SER cc_start: 0.9187 (t) cc_final: 0.8952 (p) REVERT: C 343 SER cc_start: 0.9051 (m) cc_final: 0.8600 (p) REVERT: C 397 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8166 (mt-10) REVERT: C 420 ARG cc_start: 0.8781 (mmm-85) cc_final: 0.8422 (mmm-85) REVERT: C 504 LYS cc_start: 0.9017 (ttmt) cc_final: 0.8665 (ttmm) REVERT: C 653 TYR cc_start: 0.6731 (OUTLIER) cc_final: 0.5331 (p90) REVERT: C 700 GLN cc_start: 0.8940 (tp40) cc_final: 0.8527 (tp-100) REVERT: C 716 MET cc_start: 0.5063 (ptm) cc_final: 0.4317 (ptp) REVERT: C 740 TRP cc_start: 0.8596 (m100) cc_final: 0.8336 (m100) REVERT: C 743 ARG cc_start: 0.8496 (ttm-80) cc_final: 0.7829 (tpp80) outliers start: 37 outliers final: 26 residues processed: 423 average time/residue: 0.1346 time to fit residues: 88.1392 Evaluate side-chains 417 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 388 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 653 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 136 optimal weight: 0.0270 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 59 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 202 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 393 ASN B 378 HIS C 206 HIS C 393 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.149993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.099749 restraints weight = 28996.300| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.59 r_work: 0.2973 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 18180 Z= 0.212 Angle : 0.586 8.124 24631 Z= 0.302 Chirality : 0.040 0.180 2756 Planarity : 0.003 0.039 3020 Dihedral : 8.523 85.625 2539 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.16 % Allowed : 15.24 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.88 (0.19), residues: 2136 helix: 2.75 (0.14), residues: 1276 sheet: -0.20 (0.61), residues: 76 loop : -1.27 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 557 TYR 0.024 0.001 TYR C 309 PHE 0.050 0.001 PHE D 304 TRP 0.014 0.001 TRP A 372 HIS 0.012 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 (18180) covalent geometry : angle 0.58566 / 0.30 (24631) hydrogen bonds : bond 0.04807 / 3.22 ( 996) hydrogen bonds : angle 3.93717 / 2.83 ( 2883) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 389 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 GLN cc_start: 0.8771 (mt0) cc_final: 0.8363 (mp10) REVERT: A 378 HIS cc_start: 0.7934 (p-80) cc_final: 0.7623 (p90) REVERT: A 423 GLN cc_start: 0.9087 (tp40) cc_final: 0.8821 (tp-100) REVERT: A 584 TYR cc_start: 0.8869 (t80) cc_final: 0.8575 (t80) REVERT: A 707 ASP cc_start: 0.8947 (m-30) cc_final: 0.8745 (m-30) REVERT: D 354 GLN cc_start: 0.8735 (mt0) cc_final: 0.8331 (mp10) REVERT: D 410 HIS cc_start: 0.8361 (p90) cc_final: 0.7713 (p90) REVERT: D 424 ASP cc_start: 0.9029 (t70) cc_final: 0.8690 (t70) REVERT: D 571 LYS cc_start: 0.8776 (mmtt) cc_final: 0.8474 (tptp) REVERT: D 653 TYR cc_start: 0.7343 (OUTLIER) cc_final: 0.5858 (p90) REVERT: B 324 LYS cc_start: 0.8893 (mttt) cc_final: 0.8347 (mmtt) REVERT: B 371 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7777 (tp30) REVERT: B 410 HIS cc_start: 0.7880 (m90) cc_final: 0.7671 (m-70) REVERT: B 416 GLU cc_start: 0.7795 (tp30) cc_final: 0.7528 (tp30) REVERT: B 653 TYR cc_start: 0.6685 (OUTLIER) cc_final: 0.5791 (p90) REVERT: C 222 GLU cc_start: 0.8604 (pt0) cc_final: 0.8398 (pt0) REVERT: C 342 SER cc_start: 0.9186 (t) cc_final: 0.8932 (p) REVERT: C 343 SER cc_start: 0.9083 (m) cc_final: 0.8620 (p) REVERT: C 397 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8110 (mt-10) REVERT: C 420 ARG cc_start: 0.8789 (mmm-85) cc_final: 0.8445 (mmm-85) REVERT: C 504 LYS cc_start: 0.9028 (ttmt) cc_final: 0.8679 (ttmm) REVERT: C 700 GLN cc_start: 0.8938 (tp40) cc_final: 0.8514 (tp-100) REVERT: C 716 MET cc_start: 0.5060 (ptm) cc_final: 0.4286 (ptp) REVERT: C 740 TRP cc_start: 0.8612 (m100) cc_final: 0.8309 (m100) REVERT: C 743 ARG cc_start: 0.8514 (ttm-80) cc_final: 0.7850 (tpp80) outliers start: 41 outliers final: 36 residues processed: 417 average time/residue: 0.1315 time to fit residues: 85.5687 Evaluate side-chains 416 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 378 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 741 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 126 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 199 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 22 optimal weight: 0.0670 chunk 163 optimal weight: 7.9990 chunk 201 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 211 optimal weight: 5.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 393 ASN B 378 HIS C 206 HIS C 393 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.153784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.103447 restraints weight = 28921.891| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.65 r_work: 0.3023 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18180 Z= 0.111 Angle : 0.544 8.346 24631 Z= 0.282 Chirality : 0.037 0.154 2756 Planarity : 0.003 0.039 3020 Dihedral : 8.155 84.025 2539 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.85 % Allowed : 15.88 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.97 (0.19), residues: 2136 helix: 2.90 (0.14), residues: 1256 sheet: -0.06 (0.61), residues: 76 loop : -1.28 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 575 TYR 0.050 0.001 TYR C 309 PHE 0.050 0.001 PHE D 304 TRP 0.011 0.001 TRP A 372 HIS 0.014 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (18180) covalent geometry : angle 0.54410 / 0.28 (24631) hydrogen bonds : bond 0.03949 / 2.65 ( 996) hydrogen bonds : angle 3.77302 / 2.71 ( 2883) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 410 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 GLN cc_start: 0.8754 (mt0) cc_final: 0.8348 (mp10) REVERT: A 378 HIS cc_start: 0.7889 (p-80) cc_final: 0.7581 (p90) REVERT: A 423 GLN cc_start: 0.9052 (tp40) cc_final: 0.8792 (tp-100) REVERT: A 584 TYR cc_start: 0.8743 (t80) cc_final: 0.8431 (t80) REVERT: D 354 GLN cc_start: 0.8751 (mt0) cc_final: 0.8326 (mp10) REVERT: D 410 HIS cc_start: 0.8311 (p90) cc_final: 0.7667 (p90) REVERT: D 416 GLU cc_start: 0.7600 (tp30) cc_final: 0.7357 (tp30) REVERT: D 424 ASP cc_start: 0.9010 (t70) cc_final: 0.8689 (t70) REVERT: D 536 GLU cc_start: 0.8592 (mp0) cc_final: 0.8197 (mp0) REVERT: D 571 LYS cc_start: 0.8746 (mmtt) cc_final: 0.8347 (tptp) REVERT: D 653 TYR cc_start: 0.7223 (OUTLIER) cc_final: 0.5675 (p90) REVERT: B 311 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8925 (mm-30) REVERT: B 324 LYS cc_start: 0.8859 (mttt) cc_final: 0.8328 (mmtt) REVERT: B 354 GLN cc_start: 0.8637 (mt0) cc_final: 0.8310 (mt0) REVERT: B 371 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7804 (tp30) REVERT: B 410 HIS cc_start: 0.7854 (m90) cc_final: 0.7620 (m-70) REVERT: B 420 ARG cc_start: 0.9012 (mmm-85) cc_final: 0.8770 (mmm-85) REVERT: B 483 SER cc_start: 0.9286 (t) cc_final: 0.9037 (p) REVERT: B 653 TYR cc_start: 0.6649 (OUTLIER) cc_final: 0.5730 (p90) REVERT: B 663 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9214 (mt) REVERT: B 724 LYS cc_start: 0.8690 (tmtt) cc_final: 0.8396 (tmtt) REVERT: C 222 GLU cc_start: 0.8628 (pt0) cc_final: 0.8409 (pt0) REVERT: C 342 SER cc_start: 0.9181 (t) cc_final: 0.8966 (p) REVERT: C 343 SER cc_start: 0.9012 (m) cc_final: 0.8561 (p) REVERT: C 391 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8308 (mm-30) REVERT: C 420 ARG cc_start: 0.8805 (mmm-85) cc_final: 0.8464 (mmm-85) REVERT: C 424 ASP cc_start: 0.8947 (t70) cc_final: 0.8740 (t70) REVERT: C 504 LYS cc_start: 0.9001 (ttmt) cc_final: 0.8646 (ttmm) REVERT: C 584 TYR cc_start: 0.8903 (t80) cc_final: 0.8255 (t80) REVERT: C 648 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7561 (mm-30) REVERT: C 653 TYR cc_start: 0.6728 (OUTLIER) cc_final: 0.5414 (p90) REVERT: C 700 GLN cc_start: 0.8914 (tp40) cc_final: 0.8494 (tp-100) REVERT: C 716 MET cc_start: 0.5050 (ptm) cc_final: 0.4280 (ptp) REVERT: C 743 ARG cc_start: 0.8464 (ttm-80) cc_final: 0.7697 (tpp80) outliers start: 35 outliers final: 23 residues processed: 427 average time/residue: 0.1315 time to fit residues: 87.5944 Evaluate side-chains 414 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 387 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 653 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 94 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 192 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 206 optimal weight: 4.9990 chunk 205 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 393 ASN B 378 HIS C 206 HIS C 393 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.152531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.102187 restraints weight = 28824.017| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.61 r_work: 0.3010 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18180 Z= 0.147 Angle : 0.566 8.175 24631 Z= 0.292 Chirality : 0.039 0.201 2756 Planarity : 0.003 0.038 3020 Dihedral : 8.073 84.905 2539 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.95 % Allowed : 16.35 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.95 (0.19), residues: 2136 helix: 2.85 (0.14), residues: 1256 sheet: -0.00 (0.61), residues: 76 loop : -1.24 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 575 TYR 0.015 0.001 TYR B 584 PHE 0.040 0.001 PHE D 304 TRP 0.013 0.001 TRP A 372 HIS 0.013 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (18180) covalent geometry : angle 0.56633 / 0.29 (24631) hydrogen bonds : bond 0.04218 / 2.83 ( 996) hydrogen bonds : angle 3.83185 / 2.76 ( 2883) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 394 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 GLN cc_start: 0.8787 (mt0) cc_final: 0.8376 (mp10) REVERT: A 378 HIS cc_start: 0.7938 (p-80) cc_final: 0.7627 (p90) REVERT: A 423 GLN cc_start: 0.9067 (tp40) cc_final: 0.8805 (tp-100) REVERT: A 584 TYR cc_start: 0.8784 (t80) cc_final: 0.8494 (t80) REVERT: D 354 GLN cc_start: 0.8743 (mt0) cc_final: 0.8306 (mp10) REVERT: D 410 HIS cc_start: 0.8355 (p90) cc_final: 0.7732 (p90) REVERT: D 424 ASP cc_start: 0.9012 (t70) cc_final: 0.8687 (t70) REVERT: D 571 LYS cc_start: 0.8772 (mmtt) cc_final: 0.8455 (tptp) REVERT: D 653 TYR cc_start: 0.7255 (OUTLIER) cc_final: 0.5743 (p90) REVERT: B 324 LYS cc_start: 0.8880 (mttt) cc_final: 0.8333 (mmtt) REVERT: B 354 GLN cc_start: 0.8663 (mt0) cc_final: 0.8358 (mt0) REVERT: B 371 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7771 (tp30) REVERT: B 410 HIS cc_start: 0.7855 (m90) cc_final: 0.7630 (m-70) REVERT: B 420 ARG cc_start: 0.9018 (mmm-85) cc_final: 0.8768 (mmm-85) REVERT: B 653 TYR cc_start: 0.6650 (OUTLIER) cc_final: 0.5714 (p90) REVERT: B 663 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9250 (mt) REVERT: C 222 GLU cc_start: 0.8630 (pt0) cc_final: 0.8406 (pt0) REVERT: C 342 SER cc_start: 0.9160 (t) cc_final: 0.8921 (p) REVERT: C 343 SER cc_start: 0.9035 (m) cc_final: 0.8581 (p) REVERT: C 383 ASP cc_start: 0.8246 (t0) cc_final: 0.7895 (t0) REVERT: C 385 SER cc_start: 0.9081 (t) cc_final: 0.8614 (m) REVERT: C 420 ARG cc_start: 0.8826 (mmm-85) cc_final: 0.8489 (mmm-85) REVERT: C 504 LYS cc_start: 0.9017 (ttmt) cc_final: 0.8664 (ttmm) REVERT: C 648 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7561 (mm-30) REVERT: C 653 TYR cc_start: 0.6737 (OUTLIER) cc_final: 0.5408 (p90) REVERT: C 700 GLN cc_start: 0.8927 (tp40) cc_final: 0.8503 (tp-100) REVERT: C 716 MET cc_start: 0.4922 (ptm) cc_final: 0.4207 (ptp) REVERT: C 743 ARG cc_start: 0.8444 (ttm-80) cc_final: 0.7771 (tpp80) outliers start: 37 outliers final: 29 residues processed: 416 average time/residue: 0.1356 time to fit residues: 87.2300 Evaluate side-chains 416 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 383 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 653 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 152 optimal weight: 0.9980 chunk 111 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 208 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 156 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 132 optimal weight: 0.0270 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 393 ASN B 378 HIS C 206 HIS C 259 ASN C 393 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.153387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.103462 restraints weight = 28669.392| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.64 r_work: 0.3036 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 18180 Z= 0.120 Angle : 0.576 8.789 24631 Z= 0.297 Chirality : 0.038 0.218 2756 Planarity : 0.003 0.039 3020 Dihedral : 7.885 85.546 2539 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.00 % Allowed : 16.72 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.95 (0.19), residues: 2136 helix: 2.84 (0.14), residues: 1252 sheet: 0.10 (0.62), residues: 76 loop : -1.20 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 575 TYR 0.031 0.001 TYR C 309 PHE 0.053 0.001 PHE D 304 TRP 0.012 0.001 TRP A 372 HIS 0.013 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (18180) covalent geometry : angle 0.57648 / 0.30 (24631) hydrogen bonds : bond 0.03910 / 2.61 ( 996) hydrogen bonds : angle 3.84045 / 2.76 ( 2883) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 403 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 GLN cc_start: 0.8780 (mt0) cc_final: 0.8453 (mp10) REVERT: A 378 HIS cc_start: 0.7920 (p-80) cc_final: 0.7611 (p90) REVERT: A 423 GLN cc_start: 0.9085 (tp40) cc_final: 0.8823 (tp-100) REVERT: A 464 LYS cc_start: 0.8147 (mmmt) cc_final: 0.7828 (mppt) REVERT: A 584 TYR cc_start: 0.8683 (t80) cc_final: 0.8315 (t80) REVERT: D 354 GLN cc_start: 0.8756 (mt0) cc_final: 0.8324 (mp10) REVERT: D 410 HIS cc_start: 0.8330 (p90) cc_final: 0.7710 (p90) REVERT: D 416 GLU cc_start: 0.7529 (tp30) cc_final: 0.7326 (tp30) REVERT: D 424 ASP cc_start: 0.9011 (t70) cc_final: 0.8665 (t70) REVERT: D 536 GLU cc_start: 0.8746 (mp0) cc_final: 0.8524 (mp0) REVERT: D 571 LYS cc_start: 0.8738 (mmtt) cc_final: 0.8425 (tptp) REVERT: D 653 TYR cc_start: 0.7223 (OUTLIER) cc_final: 0.5685 (p90) REVERT: D 746 GLU cc_start: 0.7888 (tt0) cc_final: 0.7593 (tt0) REVERT: B 311 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8929 (mm-30) REVERT: B 324 LYS cc_start: 0.8857 (mttt) cc_final: 0.8338 (mmtt) REVERT: B 354 GLN cc_start: 0.8603 (mt0) cc_final: 0.8255 (mt0) REVERT: B 371 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7820 (tp30) REVERT: B 410 HIS cc_start: 0.7843 (m90) cc_final: 0.7608 (m-70) REVERT: B 420 ARG cc_start: 0.9004 (mmm-85) cc_final: 0.8755 (mmm-85) REVERT: B 483 SER cc_start: 0.9286 (t) cc_final: 0.9038 (p) REVERT: B 653 TYR cc_start: 0.6702 (OUTLIER) cc_final: 0.5749 (p90) REVERT: B 663 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9219 (mt) REVERT: C 215 THR cc_start: 0.9213 (p) cc_final: 0.9002 (t) REVERT: C 222 GLU cc_start: 0.8623 (pt0) cc_final: 0.8397 (pt0) REVERT: C 342 SER cc_start: 0.9173 (t) cc_final: 0.8957 (p) REVERT: C 343 SER cc_start: 0.9005 (m) cc_final: 0.8555 (p) REVERT: C 383 ASP cc_start: 0.8236 (t0) cc_final: 0.7871 (t0) REVERT: C 385 SER cc_start: 0.9036 (t) cc_final: 0.8555 (m) REVERT: C 420 ARG cc_start: 0.8830 (mmm-85) cc_final: 0.8498 (mmm-85) REVERT: C 504 LYS cc_start: 0.8992 (ttmt) cc_final: 0.8639 (ttmm) REVERT: C 584 TYR cc_start: 0.8892 (t80) cc_final: 0.8270 (t80) REVERT: C 648 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7572 (mm-30) REVERT: C 653 TYR cc_start: 0.6716 (OUTLIER) cc_final: 0.5371 (p90) REVERT: C 716 MET cc_start: 0.4877 (ptm) cc_final: 0.4171 (ptp) REVERT: C 743 ARG cc_start: 0.8455 (ttm-80) cc_final: 0.7705 (tpp80) outliers start: 38 outliers final: 30 residues processed: 422 average time/residue: 0.1350 time to fit residues: 88.7202 Evaluate side-chains 424 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 390 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 653 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 1 optimal weight: 9.9990 chunk 194 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 182 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 209 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 144 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 378 HIS C 206 HIS C 259 ASN C 700 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.154108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.103464 restraints weight = 28943.160| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.66 r_work: 0.3033 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 18180 Z= 0.178 Angle : 0.768 59.142 24631 Z= 0.438 Chirality : 0.039 0.395 2756 Planarity : 0.003 0.058 3020 Dihedral : 7.898 85.571 2539 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.06 % Favored : 94.90 % Rotamer: Outliers : 2.11 % Allowed : 16.72 % Favored : 81.17 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 7.14 % 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: 1.94 (0.19), residues: 2136 helix: 2.82 (0.14), residues: 1252 sheet: 0.10 (0.62), residues: 76 loop : -1.20 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 211 TYR 0.015 0.001 TYR C 309 PHE 0.050 0.001 PHE D 304 TRP 0.012 0.001 TRP A 372 HIS 0.012 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (18180) covalent geometry : angle 0.76775 / 0.44 (24631) hydrogen bonds : bond 0.03978 / 2.66 ( 996) hydrogen bonds : angle 3.85873 / 2.77 ( 2883) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4240.62 seconds wall clock time: 73 minutes 39.65 seconds (4419.65 seconds total)