Starting phenix.real_space_refine on Fri Jan 17 22:23:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qzc_18774/01_2025/8qzc_18774.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qzc_18774/01_2025/8qzc_18774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qzc_18774/01_2025/8qzc_18774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qzc_18774/01_2025/8qzc_18774.map" model { file = "/net/cci-nas-00/data/ceres_data/8qzc_18774/01_2025/8qzc_18774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qzc_18774/01_2025/8qzc_18774.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 Ca 4 9.91 5 S 72 5.16 5 C 7472 2.51 5 N 1888 2.21 5 O 2032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 11468 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5732 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 30, 'TRANS': 670} Chain breaks: 4 Chain: "B" Number of atoms: 5732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5732 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 30, 'TRANS': 670} Chain breaks: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.33, per 1000 atoms: 0.64 Number of scatterers: 11468 At special positions: 0 Unit cell: (90.283, 121.915, 113.348, 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) Ca 4 19.99 S 72 16.00 O 2032 8.00 N 1888 7.00 C 7472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 836 " distance=2.04 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 386 " distance=2.02 Simple disulfide: pdb=" SG CYS A 625 " - pdb=" SG CYS A 630 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 836 " distance=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 386 " distance=2.02 Simple disulfide: pdb=" SG CYS B 625 " - pdb=" SG CYS B 630 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.5 seconds 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 10 sheets defined 67.4% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 166 through 180 removed outlier: 4.041A pdb=" N MET A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.643A pdb=" N LYS A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS A 212 " --> pdb=" O LYS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 226 removed outlier: 3.648A pdb=" N SER A 225 " --> pdb=" O TYR A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.672A pdb=" N PHE A 240 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 241 " --> pdb=" O ASP A 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 237 through 241' Processing helix chain 'A' and resid 242 through 257 Processing helix chain 'A' and resid 268 through 275 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 307 through 311 removed outlier: 3.650A pdb=" N VAL A 310 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE A 311 " --> pdb=" O TYR A 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 307 through 311' Processing helix chain 'A' and resid 316 through 358 removed outlier: 7.524A pdb=" N GLU A 326 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N LYS A 327 " --> pdb=" O TYR A 323 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 343 " --> pdb=" O THR A 339 " (cutoff:3.500A) Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 359 through 362 Processing helix chain 'A' and resid 363 through 371 Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 394 through 402 removed outlier: 3.665A pdb=" N ALA A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 405 No H-bonds generated for 'chain 'A' and resid 403 through 405' Processing helix chain 'A' and resid 406 through 439 removed outlier: 3.531A pdb=" N VAL A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 465 Processing helix chain 'A' and resid 489 through 527 removed outlier: 3.724A pdb=" N ALA A 519 " --> pdb=" O ARG A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 569 removed outlier: 4.070A pdb=" N GLU A 555 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 569 " --> pdb=" O THR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 601 Proline residue: A 595 - end of helix Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 630 through 651 removed outlier: 3.937A pdb=" N LYS A 645 " --> pdb=" O ILE A 641 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN A 646 " --> pdb=" O MET A 642 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN A 649 " --> pdb=" O LYS A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 693 removed outlier: 3.728A pdb=" N VAL A 689 " --> pdb=" O GLN A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 716 removed outlier: 3.652A pdb=" N GLU A 705 " --> pdb=" O PRO A 701 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 716 " --> pdb=" O PHE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 744 removed outlier: 3.938A pdb=" N VAL A 733 " --> pdb=" O LEU A 729 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG A 736 " --> pdb=" O ILE A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.933A pdb=" N ASN A 762 " --> pdb=" O GLY A 758 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A 772 " --> pdb=" O GLY A 768 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 795 Processing helix chain 'A' and resid 803 through 809 Processing helix chain 'A' and resid 815 through 817 No H-bonds generated for 'chain 'A' and resid 815 through 817' Processing helix chain 'A' and resid 854 through 886 removed outlier: 3.783A pdb=" N TRP A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 910 removed outlier: 3.906A pdb=" N ARG A 910 " --> pdb=" O GLU A 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 181 removed outlier: 4.011A pdb=" N MET B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Proline residue: B 177 - end of helix Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 205 through 213 removed outlier: 3.847A pdb=" N HIS B 212 " --> pdb=" O LYS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 226 removed outlier: 3.543A pdb=" N SER B 225 " --> pdb=" O TYR B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 241 removed outlier: 3.726A pdb=" N PHE B 240 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE B 241 " --> pdb=" O ASP B 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 237 through 241' Processing helix chain 'B' and resid 242 through 257 Processing helix chain 'B' and resid 268 through 275 Processing helix chain 'B' and resid 296 through 305 Processing helix chain 'B' and resid 307 through 311 removed outlier: 3.631A pdb=" N VAL B 310 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE B 311 " --> pdb=" O TYR B 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 307 through 311' Processing helix chain 'B' and resid 316 through 358 removed outlier: 7.512A pdb=" N GLU B 326 " --> pdb=" O LYS B 322 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N LYS B 327 " --> pdb=" O TYR B 323 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL B 328 " --> pdb=" O PHE B 324 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) Proline residue: B 344 - end of helix Processing helix chain 'B' and resid 359 through 362 Processing helix chain 'B' and resid 363 through 371 Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.662A pdb=" N ALA B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing helix chain 'B' and resid 406 through 439 removed outlier: 3.523A pdb=" N VAL B 410 " --> pdb=" O ASN B 406 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 465 Processing helix chain 'B' and resid 489 through 527 removed outlier: 3.715A pdb=" N ALA B 519 " --> pdb=" O ARG B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 569 removed outlier: 4.068A pdb=" N GLU B 555 " --> pdb=" O ILE B 551 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL B 556 " --> pdb=" O LEU B 552 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 569 " --> pdb=" O THR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 601 Proline residue: B 595 - end of helix Processing helix chain 'B' and resid 617 through 619 No H-bonds generated for 'chain 'B' and resid 617 through 619' Processing helix chain 'B' and resid 630 through 651 removed outlier: 3.959A pdb=" N LYS B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN B 646 " --> pdb=" O MET B 642 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN B 649 " --> pdb=" O LYS B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 693 removed outlier: 3.701A pdb=" N VAL B 689 " --> pdb=" O GLN B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 716 removed outlier: 3.655A pdb=" N GLU B 705 " --> pdb=" O PRO B 701 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 716 " --> pdb=" O PHE B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 744 removed outlier: 3.921A pdb=" N VAL B 733 " --> pdb=" O LEU B 729 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG B 736 " --> pdb=" O ILE B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.942A pdb=" N ASN B 762 " --> pdb=" O GLY B 758 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 772 " --> pdb=" O GLY B 768 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE B 773 " --> pdb=" O LYS B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 795 Processing helix chain 'B' and resid 803 through 809 Processing helix chain 'B' and resid 815 through 817 No H-bonds generated for 'chain 'B' and resid 815 through 817' Processing helix chain 'B' and resid 854 through 886 removed outlier: 3.780A pdb=" N TRP B 858 " --> pdb=" O SER B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 910 removed outlier: 3.893A pdb=" N ARG B 910 " --> pdb=" O GLU B 906 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 126 removed outlier: 3.893A pdb=" N ALA A 279 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 190 removed outlier: 3.525A pdb=" N THR A 187 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 217 through 218 Processing sheet with id=AA4, first strand: chain 'A' and resid 615 through 616 Processing sheet with id=AA5, first strand: chain 'A' and resid 810 through 813 Processing sheet with id=AA6, first strand: chain 'B' and resid 124 through 126 removed outlier: 3.939A pdb=" N ALA B 279 " --> pdb=" O PHE B 126 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 190 removed outlier: 3.583A pdb=" N THR B 187 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 217 through 218 Processing sheet with id=AA9, first strand: chain 'B' and resid 615 through 616 Processing sheet with id=AB1, first strand: chain 'B' and resid 810 through 813 661 hydrogen bonds defined for protein. 1947 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.52 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3562 1.34 - 1.46: 2914 1.46 - 1.58: 5160 1.58 - 1.70: 0 1.70 - 1.82: 118 Bond restraints: 11754 Sorted by residual: bond pdb=" CB GLU A 555 " pdb=" CG GLU A 555 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.14e+00 bond pdb=" CB GLU B 555 " pdb=" CG GLU B 555 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.10e+00 bond pdb=" SD MET A 416 " pdb=" CE MET A 416 " ideal model delta sigma weight residual 1.791 1.755 0.036 2.50e-02 1.60e+03 2.02e+00 bond pdb=" SD MET B 416 " pdb=" CE MET B 416 " ideal model delta sigma weight residual 1.791 1.756 0.035 2.50e-02 1.60e+03 2.01e+00 bond pdb=" CB ASP B 883 " pdb=" CG ASP B 883 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.75e+00 ... (remaining 11749 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 15678 2.68 - 5.37: 178 5.37 - 8.05: 44 8.05 - 10.74: 6 10.74 - 13.42: 6 Bond angle restraints: 15912 Sorted by residual: angle pdb=" CB MET A 424 " pdb=" CG MET A 424 " pdb=" SD MET A 424 " ideal model delta sigma weight residual 112.70 124.93 -12.23 3.00e+00 1.11e-01 1.66e+01 angle pdb=" C TYR B 288 " pdb=" N GLU B 289 " pdb=" CA GLU B 289 " ideal model delta sigma weight residual 122.08 127.90 -5.82 1.47e+00 4.63e-01 1.56e+01 angle pdb=" CB MET B 424 " pdb=" CG MET B 424 " pdb=" SD MET B 424 " ideal model delta sigma weight residual 112.70 124.42 -11.72 3.00e+00 1.11e-01 1.53e+01 angle pdb=" C TYR A 288 " pdb=" N GLU A 289 " pdb=" CA GLU A 289 " ideal model delta sigma weight residual 122.08 127.81 -5.73 1.47e+00 4.63e-01 1.52e+01 angle pdb=" CA LEU B 191 " pdb=" CB LEU B 191 " pdb=" CG LEU B 191 " ideal model delta sigma weight residual 116.30 129.72 -13.42 3.50e+00 8.16e-02 1.47e+01 ... (remaining 15907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 6166 16.03 - 32.06: 702 32.06 - 48.08: 127 48.08 - 64.11: 21 64.11 - 80.14: 6 Dihedral angle restraints: 7022 sinusoidal: 2870 harmonic: 4152 Sorted by residual: dihedral pdb=" CB CYS B 382 " pdb=" SG CYS B 382 " pdb=" SG CYS B 386 " pdb=" CB CYS B 386 " ideal model delta sinusoidal sigma weight residual -86.00 -149.60 63.60 1 1.00e+01 1.00e-02 5.33e+01 dihedral pdb=" CB CYS A 382 " pdb=" SG CYS A 382 " pdb=" SG CYS A 386 " pdb=" CB CYS A 386 " ideal model delta sinusoidal sigma weight residual -86.00 -149.37 63.37 1 1.00e+01 1.00e-02 5.30e+01 dihedral pdb=" CB CYS B 625 " pdb=" SG CYS B 625 " pdb=" SG CYS B 630 " pdb=" CB CYS B 630 " ideal model delta sinusoidal sigma weight residual -86.00 -46.12 -39.88 1 1.00e+01 1.00e-02 2.23e+01 ... (remaining 7019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1314 0.051 - 0.102: 352 0.102 - 0.154: 80 0.154 - 0.205: 3 0.205 - 0.256: 5 Chirality restraints: 1754 Sorted by residual: chirality pdb=" CA GLU B 425 " pdb=" N GLU B 425 " pdb=" C GLU B 425 " pdb=" CB GLU B 425 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB VAL A 569 " pdb=" CA VAL A 569 " pdb=" CG1 VAL A 569 " pdb=" CG2 VAL A 569 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB VAL B 750 " pdb=" CA VAL B 750 " pdb=" CG1 VAL B 750 " pdb=" CG2 VAL B 750 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1751 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 176 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.32e+00 pdb=" N PRO A 177 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 177 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 177 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 176 " 0.037 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO B 177 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 177 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 177 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 406 " -0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO B 407 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 407 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 407 " -0.025 5.00e-02 4.00e+02 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2328 2.78 - 3.31: 10850 3.31 - 3.84: 18851 3.84 - 4.37: 21116 4.37 - 4.90: 37307 Nonbonded interactions: 90452 Sorted by model distance: nonbonded pdb=" O VAL B 590 " pdb=" OG1 THR B 594 " model vdw 2.246 3.040 nonbonded pdb=" O VAL A 590 " pdb=" OG1 THR A 594 " model vdw 2.249 3.040 nonbonded pdb=" O LYS A 175 " pdb=" OG1 THR A 178 " model vdw 2.290 3.040 nonbonded pdb=" OG SER A 387 " pdb=" OD2 ASP A 828 " model vdw 2.290 3.040 nonbonded pdb=" OG SER B 387 " pdb=" OD2 ASP B 828 " model vdw 2.291 3.040 ... (remaining 90447 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.780 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: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 27.400 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 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 : 0.004 0.047 11754 Z= 0.246 Angle : 0.813 13.424 15912 Z= 0.420 Chirality : 0.049 0.256 1754 Planarity : 0.006 0.058 1998 Dihedral : 13.360 80.141 4310 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.20), residues: 1382 helix: -0.05 (0.16), residues: 856 sheet: -1.79 (0.99), residues: 28 loop : -2.35 (0.24), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 427 HIS 0.004 0.001 HIS A 230 PHE 0.028 0.002 PHE B 324 TYR 0.026 0.002 TYR B 222 ARG 0.007 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.346 Fit side-chains REVERT: A 827 LEU cc_start: 0.7498 (mt) cc_final: 0.7217 (mp) REVERT: A 909 MET cc_start: 0.5081 (ttm) cc_final: 0.3630 (tpt) REVERT: B 827 LEU cc_start: 0.7553 (mt) cc_final: 0.7310 (mp) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.2489 time to fit residues: 60.8993 Evaluate side-chains 130 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.188321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.144282 restraints weight = 13899.488| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.88 r_work: 0.3595 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11754 Z= 0.269 Angle : 0.609 8.552 15912 Z= 0.317 Chirality : 0.042 0.198 1754 Planarity : 0.004 0.048 1998 Dihedral : 4.273 16.034 1546 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.72 % Allowed : 7.69 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.22), residues: 1382 helix: 0.91 (0.17), residues: 854 sheet: -2.84 (0.59), residues: 58 loop : -2.02 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 427 HIS 0.008 0.001 HIS B 402 PHE 0.018 0.002 PHE A 126 TYR 0.015 0.002 TYR B 838 ARG 0.004 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 1.339 Fit side-chains REVERT: A 215 GLN cc_start: 0.7388 (pp30) cc_final: 0.6409 (pp30) REVERT: A 691 PHE cc_start: 0.8419 (t80) cc_final: 0.8215 (t80) REVERT: A 752 ILE cc_start: 0.8232 (tt) cc_final: 0.7593 (mm) REVERT: B 215 GLN cc_start: 0.7491 (pp30) cc_final: 0.7236 (pt0) REVERT: B 752 ILE cc_start: 0.8219 (tt) cc_final: 0.7582 (mm) outliers start: 9 outliers final: 7 residues processed: 152 average time/residue: 0.2421 time to fit residues: 53.6319 Evaluate side-chains 139 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 733 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 105 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.186533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.143403 restraints weight = 13968.417| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.91 r_work: 0.3567 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11754 Z= 0.268 Angle : 0.605 8.000 15912 Z= 0.314 Chirality : 0.043 0.191 1754 Planarity : 0.004 0.044 1998 Dihedral : 4.223 15.184 1546 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.28 % Allowed : 9.94 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.22), residues: 1382 helix: 1.15 (0.17), residues: 854 sheet: -3.07 (0.58), residues: 58 loop : -2.01 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 427 HIS 0.005 0.001 HIS A 402 PHE 0.028 0.002 PHE A 126 TYR 0.015 0.002 TYR A 838 ARG 0.002 0.000 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 1.272 Fit side-chains REVERT: A 215 GLN cc_start: 0.7308 (pp30) cc_final: 0.6345 (pp30) REVERT: A 752 ILE cc_start: 0.8272 (tt) cc_final: 0.7664 (mm) REVERT: B 215 GLN cc_start: 0.7470 (pp30) cc_final: 0.7247 (pt0) REVERT: B 752 ILE cc_start: 0.8198 (tt) cc_final: 0.7542 (mm) outliers start: 16 outliers final: 10 residues processed: 147 average time/residue: 0.2392 time to fit residues: 51.4893 Evaluate side-chains 141 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 733 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 78 optimal weight: 0.0030 chunk 14 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 2 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.195838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.156683 restraints weight = 14159.013| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 1.78 r_work: 0.3727 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11754 Z= 0.159 Angle : 0.555 7.842 15912 Z= 0.284 Chirality : 0.040 0.195 1754 Planarity : 0.003 0.043 1998 Dihedral : 4.124 22.244 1546 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.64 % Allowed : 11.30 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.22), residues: 1382 helix: 1.48 (0.17), residues: 854 sheet: -3.11 (0.57), residues: 58 loop : -1.93 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 427 HIS 0.004 0.001 HIS B 402 PHE 0.028 0.001 PHE A 126 TYR 0.010 0.001 TYR B 838 ARG 0.002 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 1.219 Fit side-chains REVERT: A 215 GLN cc_start: 0.7269 (pp30) cc_final: 0.6931 (pt0) REVERT: A 691 PHE cc_start: 0.8462 (t80) cc_final: 0.8178 (t80) REVERT: A 706 MET cc_start: 0.8577 (mmp) cc_final: 0.8302 (mmp) REVERT: A 752 ILE cc_start: 0.8354 (tt) cc_final: 0.7798 (mm) REVERT: A 909 MET cc_start: 0.4867 (ttm) cc_final: 0.3574 (tpt) REVERT: B 215 GLN cc_start: 0.7544 (pp30) cc_final: 0.7254 (pt0) REVERT: B 706 MET cc_start: 0.8568 (mmp) cc_final: 0.8299 (mmp) REVERT: B 752 ILE cc_start: 0.8265 (tt) cc_final: 0.7672 (mm) outliers start: 8 outliers final: 4 residues processed: 147 average time/residue: 0.2483 time to fit residues: 52.7184 Evaluate side-chains 136 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 616 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 76 optimal weight: 8.9990 chunk 118 optimal weight: 0.0170 chunk 128 optimal weight: 3.9990 chunk 99 optimal weight: 0.0020 chunk 114 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 overall best weight: 0.7630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.195834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.157364 restraints weight = 14164.689| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 1.94 r_work: 0.3712 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11754 Z= 0.174 Angle : 0.549 8.052 15912 Z= 0.281 Chirality : 0.040 0.183 1754 Planarity : 0.003 0.042 1998 Dihedral : 4.024 19.501 1546 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.44 % Allowed : 11.94 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.22), residues: 1382 helix: 1.64 (0.17), residues: 854 sheet: -3.15 (0.58), residues: 58 loop : -1.86 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 427 HIS 0.004 0.001 HIS A 402 PHE 0.027 0.001 PHE A 126 TYR 0.011 0.001 TYR A 687 ARG 0.002 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 1.399 Fit side-chains REVERT: A 126 PHE cc_start: 0.6752 (t80) cc_final: 0.6549 (t80) REVERT: A 215 GLN cc_start: 0.7238 (pp30) cc_final: 0.6964 (pt0) REVERT: A 691 PHE cc_start: 0.8452 (t80) cc_final: 0.8207 (t80) REVERT: A 706 MET cc_start: 0.8591 (mmp) cc_final: 0.8378 (mmp) REVERT: A 752 ILE cc_start: 0.8378 (tt) cc_final: 0.7816 (mm) REVERT: A 909 MET cc_start: 0.4807 (ttm) cc_final: 0.3543 (tpt) REVERT: B 706 MET cc_start: 0.8604 (mmp) cc_final: 0.8394 (mmp) REVERT: B 752 ILE cc_start: 0.8299 (tt) cc_final: 0.7704 (mm) outliers start: 18 outliers final: 13 residues processed: 158 average time/residue: 0.2457 time to fit residues: 56.4011 Evaluate side-chains 145 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 757 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 57 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 88 optimal weight: 0.0870 chunk 4 optimal weight: 0.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.196282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.157710 restraints weight = 14274.729| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 1.95 r_work: 0.3714 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11754 Z= 0.165 Angle : 0.549 8.488 15912 Z= 0.281 Chirality : 0.040 0.166 1754 Planarity : 0.003 0.043 1998 Dihedral : 3.947 17.701 1546 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.04 % Allowed : 13.14 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.23), residues: 1382 helix: 1.74 (0.18), residues: 854 sheet: -3.22 (0.59), residues: 58 loop : -1.85 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 427 HIS 0.003 0.001 HIS A 402 PHE 0.022 0.001 PHE A 126 TYR 0.011 0.001 TYR A 687 ARG 0.003 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 1.388 Fit side-chains REVERT: A 215 GLN cc_start: 0.7197 (pp30) cc_final: 0.6974 (pt0) REVERT: A 691 PHE cc_start: 0.8444 (t80) cc_final: 0.8212 (t80) REVERT: A 752 ILE cc_start: 0.8364 (tt) cc_final: 0.7801 (mm) REVERT: A 909 MET cc_start: 0.4773 (ttm) cc_final: 0.3494 (tpt) REVERT: B 706 MET cc_start: 0.8592 (mmp) cc_final: 0.8250 (mmp) outliers start: 13 outliers final: 12 residues processed: 150 average time/residue: 0.2358 time to fit residues: 51.7499 Evaluate side-chains 145 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 757 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 87 optimal weight: 2.9990 chunk 74 optimal weight: 0.0270 chunk 108 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.196151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.152678 restraints weight = 14255.222| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.03 r_work: 0.3721 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11754 Z= 0.170 Angle : 0.550 8.572 15912 Z= 0.279 Chirality : 0.040 0.162 1754 Planarity : 0.003 0.043 1998 Dihedral : 3.921 16.788 1546 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.44 % Allowed : 13.62 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.23), residues: 1382 helix: 1.79 (0.18), residues: 854 sheet: -3.22 (0.59), residues: 58 loop : -1.81 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 427 HIS 0.004 0.001 HIS B 402 PHE 0.020 0.001 PHE A 126 TYR 0.012 0.001 TYR A 687 ARG 0.002 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 1.226 Fit side-chains REVERT: A 909 MET cc_start: 0.4772 (ttm) cc_final: 0.3528 (tpt) outliers start: 18 outliers final: 16 residues processed: 147 average time/residue: 0.2568 time to fit residues: 54.3309 Evaluate side-chains 143 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 757 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 55 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 chunk 84 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 ASN ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.191884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.153415 restraints weight = 14303.737| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.00 r_work: 0.3659 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11754 Z= 0.287 Angle : 0.621 9.018 15912 Z= 0.320 Chirality : 0.042 0.165 1754 Planarity : 0.004 0.043 1998 Dihedral : 4.154 17.672 1546 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.60 % Allowed : 13.70 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.22), residues: 1382 helix: 1.52 (0.17), residues: 852 sheet: -3.23 (0.61), residues: 58 loop : -1.87 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 427 HIS 0.005 0.001 HIS A 402 PHE 0.021 0.002 PHE A 126 TYR 0.016 0.002 TYR B 838 ARG 0.003 0.000 ARG B 748 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 1.220 Fit side-chains REVERT: A 175 LYS cc_start: 0.7921 (tptm) cc_final: 0.7331 (ttpp) REVERT: A 752 ILE cc_start: 0.8465 (tt) cc_final: 0.7880 (mm) REVERT: B 183 HIS cc_start: 0.4565 (OUTLIER) cc_final: 0.4322 (p90) outliers start: 20 outliers final: 18 residues processed: 145 average time/residue: 0.2319 time to fit residues: 49.2572 Evaluate side-chains 147 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 757 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 84 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 ASN ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.190597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.152314 restraints weight = 14334.767| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 1.99 r_work: 0.3641 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11754 Z= 0.317 Angle : 0.648 9.215 15912 Z= 0.334 Chirality : 0.044 0.201 1754 Planarity : 0.004 0.032 1998 Dihedral : 4.300 19.946 1546 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.52 % Allowed : 14.18 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.22), residues: 1382 helix: 1.35 (0.17), residues: 852 sheet: -3.40 (0.58), residues: 58 loop : -1.92 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 427 HIS 0.006 0.001 HIS B 402 PHE 0.029 0.002 PHE A 126 TYR 0.017 0.002 TYR A 838 ARG 0.003 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.319 Fit side-chains REVERT: A 175 LYS cc_start: 0.8097 (tptm) cc_final: 0.7469 (ttpp) REVERT: A 752 ILE cc_start: 0.8474 (tt) cc_final: 0.7882 (mm) REVERT: B 254 LEU cc_start: 0.8100 (mp) cc_final: 0.7888 (mp) outliers start: 19 outliers final: 18 residues processed: 142 average time/residue: 0.2305 time to fit residues: 48.0445 Evaluate side-chains 144 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 82 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN B 206 GLN B 692 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.192658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.153877 restraints weight = 14282.178| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 1.82 r_work: 0.3686 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11754 Z= 0.229 Angle : 0.601 9.408 15912 Z= 0.308 Chirality : 0.042 0.219 1754 Planarity : 0.003 0.032 1998 Dihedral : 4.176 17.609 1546 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.36 % Allowed : 14.34 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.22), residues: 1382 helix: 1.47 (0.17), residues: 858 sheet: -3.41 (0.57), residues: 58 loop : -2.00 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 427 HIS 0.005 0.001 HIS B 402 PHE 0.039 0.001 PHE A 126 TYR 0.013 0.001 TYR A 838 ARG 0.003 0.000 ARG B 399 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 1.211 Fit side-chains REVERT: A 175 LYS cc_start: 0.8130 (tptm) cc_final: 0.7502 (ttpp) REVERT: A 752 ILE cc_start: 0.8427 (tt) cc_final: 0.7861 (mm) REVERT: A 909 MET cc_start: 0.4839 (ttm) cc_final: 0.3659 (tpt) outliers start: 17 outliers final: 15 residues processed: 144 average time/residue: 0.2345 time to fit residues: 50.0556 Evaluate side-chains 144 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 757 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 138 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 692 ASN B 692 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.194305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.151588 restraints weight = 14154.654| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.90 r_work: 0.3725 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11754 Z= 0.187 Angle : 0.593 10.547 15912 Z= 0.300 Chirality : 0.041 0.226 1754 Planarity : 0.003 0.031 1998 Dihedral : 4.079 22.103 1546 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.28 % Allowed : 14.58 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.22), residues: 1382 helix: 1.61 (0.17), residues: 860 sheet: -3.48 (0.54), residues: 60 loop : -1.93 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 427 HIS 0.004 0.001 HIS B 402 PHE 0.036 0.001 PHE A 126 TYR 0.010 0.001 TYR A 838 ARG 0.004 0.000 ARG A 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6067.71 seconds wall clock time: 111 minutes 16.64 seconds (6676.64 seconds total)