Starting phenix.real_space_refine on Fri Sep 11 22:12:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6p2r_20240/09_2026/6p2r_20240.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p2r_20240/09_2026/6p2r_20240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6p2r_20240/09_2026/6p2r_20240.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6p2r_20240/09_2026/6p2r_20240.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6p2r_20240/09_2026/6p2r_20240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p2r_20240/09_2026/6p2r_20240.map" model { file = "/net/cci-nas-00/data/ceres_data/6p2r_20240/09_2026/6p2r_20240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p2r_20240/09_2026/6p2r_20240.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 3 5.49 5 S 62 5.16 5 C 7721 2.51 5 N 1888 2.21 5 O 2038 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11712 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5879 Classifications: {'peptide': 731} Link IDs: {'PTRANS': 31, 'TRANS': 699} Chain breaks: 1 Chain: "B" Number of atoms: 5605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5605 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 31, 'TRANS': 658} Chain breaks: 1 Chain: "A" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 111 Unusual residues: {'CPL': 1, 'NAG': 1, 'NNM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 117 Unusual residues: {'CPL': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.69, per 1000 atoms: 0.23 Number of scatterers: 11712 At special positions: 0 Unit cell: (109.074, 107.016, 108.045, 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 62 16.00 P 3 15.00 O 2038 8.00 N 1888 7.00 C 7721 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 511 " distance=2.04 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 Links applied NAG-ASN " NAG A1001 " - " ASN A 390 " " NAG B1001 " - " ASN B 131 " Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 545.2 milliseconds 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2654 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 12 sheets defined 52.1% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 35 through 42 removed outlier: 3.689A pdb=" N ALA A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 64 removed outlier: 3.994A pdb=" N LYS A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 91 Processing helix chain 'A' and resid 100 through 113 removed outlier: 4.886A pdb=" N TYR A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 160 removed outlier: 4.479A pdb=" N VAL A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 Processing helix chain 'A' and resid 176 through 185 removed outlier: 3.952A pdb=" N TYR A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 208 removed outlier: 3.778A pdb=" N MET A 208 " --> pdb=" O LYS A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 232 Processing helix chain 'A' and resid 236 through 258 removed outlier: 3.569A pdb=" N THR A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 296 removed outlier: 4.163A pdb=" N VAL A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) Proline residue: A 281 - end of helix Processing helix chain 'A' and resid 300 through 305 removed outlier: 3.716A pdb=" N ALA A 303 " --> pdb=" O GLY A 300 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A 304 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE A 305 " --> pdb=" O GLY A 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 300 through 305' Processing helix chain 'A' and resid 438 through 441 Processing helix chain 'A' and resid 504 through 507 removed outlier: 3.544A pdb=" N THR A 507 " --> pdb=" O HIS A 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 504 through 507' Processing helix chain 'A' and resid 532 through 550 Processing helix chain 'A' and resid 560 through 564 Processing helix chain 'A' and resid 586 through 613 removed outlier: 4.328A pdb=" N ALA A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 640 Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 652 through 655 Processing helix chain 'A' and resid 656 through 677 removed outlier: 3.719A pdb=" N PHE A 662 " --> pdb=" O PRO A 658 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 677 " --> pdb=" O ILE A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 704 removed outlier: 3.656A pdb=" N GLY A 686 " --> pdb=" O LYS A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 708 Processing helix chain 'A' and resid 714 through 722 removed outlier: 3.917A pdb=" N LYS A 720 " --> pdb=" O GLU A 716 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN A 722 " --> pdb=" O CYS A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.688A pdb=" N GLU A 740 " --> pdb=" O SER A 737 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR A 741 " --> pdb=" O LEU A 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 80 Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 82 through 86 removed outlier: 3.915A pdb=" N ILE B 85 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASN B 86 " --> pdb=" O ILE B 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 82 through 86' Processing helix chain 'B' and resid 92 through 105 removed outlier: 3.652A pdb=" N LYS B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR B 103 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 104 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 127 removed outlier: 4.574A pdb=" N LYS B 118 " --> pdb=" O PRO B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 173 removed outlier: 3.974A pdb=" N MET B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) Proline residue: B 164 - end of helix Processing helix chain 'B' and resid 177 through 189 Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 202 through 222 Processing helix chain 'B' and resid 229 through 250 removed outlier: 3.726A pdb=" N LYS B 250 " --> pdb=" O THR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 273 removed outlier: 3.716A pdb=" N ILE B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA B 273 " --> pdb=" O TRP B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 294 Processing helix chain 'B' and resid 294 through 312 removed outlier: 3.503A pdb=" N PHE B 301 " --> pdb=" O PRO B 297 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 312 " --> pdb=" O HIS B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 removed outlier: 3.748A pdb=" N ASN B 321 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET B 322 " --> pdb=" O ASP B 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 318 through 322' Processing helix chain 'B' and resid 323 through 330 removed outlier: 3.520A pdb=" N LEU B 330 " --> pdb=" O PHE B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 387 Processing helix chain 'B' and resid 453 through 456 removed outlier: 3.755A pdb=" N ASP B 456 " --> pdb=" O ASP B 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 453 through 456' Processing helix chain 'B' and resid 500 through 504 Processing helix chain 'B' and resid 547 through 565 Processing helix chain 'B' and resid 579 through 583 Processing helix chain 'B' and resid 610 through 623 Processing helix chain 'B' and resid 624 through 634 Processing helix chain 'B' and resid 641 through 652 Processing helix chain 'B' and resid 652 through 669 Proline residue: B 665 - end of helix Processing helix chain 'B' and resid 674 through 677 Processing helix chain 'B' and resid 678 through 695 removed outlier: 3.719A pdb=" N TYR B 683 " --> pdb=" O LEU B 679 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE B 684 " --> pdb=" O PRO B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 702 removed outlier: 5.050A pdb=" N LYS B 699 " --> pdb=" O GLY B 696 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG B 702 " --> pdb=" O LYS B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 728 Processing helix chain 'B' and resid 729 through 734 Processing helix chain 'B' and resid 740 through 744 removed outlier: 3.805A pdb=" N ARG B 743 " --> pdb=" O SER B 740 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR B 744 " --> pdb=" O ASN B 741 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 740 through 744' Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 323 through 324 Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 337 removed outlier: 4.348A pdb=" N ASN A 514 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE A 332 " --> pdb=" O ASN A 514 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 345 through 351 removed outlier: 3.938A pdb=" N HIS A 348 " --> pdb=" O GLN A 360 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN A 360 " --> pdb=" O HIS A 348 " (cutoff:3.500A) removed outlier: 16.475A pdb=" N GLN A 359 " --> pdb=" O CYS A 498 " (cutoff:3.500A) removed outlier: 12.037A pdb=" N CYS A 498 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N SER A 361 " --> pdb=" O VAL A 496 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 345 through 351 removed outlier: 3.938A pdb=" N HIS A 348 " --> pdb=" O GLN A 360 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN A 360 " --> pdb=" O HIS A 348 " (cutoff:3.500A) removed outlier: 16.475A pdb=" N GLN A 359 " --> pdb=" O CYS A 498 " (cutoff:3.500A) removed outlier: 12.037A pdb=" N CYS A 498 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N SER A 361 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLN A 493 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL A 484 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLU A 495 " --> pdb=" O HIS A 482 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N HIS A 482 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 571 through 576 removed outlier: 6.352A pdb=" N VAL A 581 " --> pdb=" O TYR A 573 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY A 575 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ARG A 579 " --> pdb=" O GLY A 575 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 348 through 353 removed outlier: 6.440A pdb=" N VAL B 348 " --> pdb=" O HIS B 529 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N HIS B 529 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N SER B 350 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 360 through 362 Processing sheet with id=AA9, first strand: chain 'B' and resid 375 through 376 removed outlier: 4.307A pdb=" N GLU B 442 " --> pdb=" O HIS B 430 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 375 through 376 removed outlier: 4.432A pdb=" N TRP B 441 " --> pdb=" O CYS B 511 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N CYS B 511 " --> pdb=" O TRP B 441 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 389 through 392 Processing sheet with id=AB3, first strand: chain 'B' and resid 458 through 465 removed outlier: 3.635A pdb=" N LYS B 484 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER B 480 " --> pdb=" O MET B 463 " (cutoff:3.500A) 553 hydrogen bonds defined for protein. 1566 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.91 Time building geometry restraints manager: 1.09 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: 1747 1.30 - 1.43: 3697 1.43 - 1.56: 6513 1.56 - 1.69: 13 1.69 - 1.82: 105 Bond restraints: 12075 Sorted by residual: bond pdb=" C18 NNM A1003 " pdb=" C19 NNM A1003 " ideal model delta sigma weight residual 1.332 1.562 -0.230 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C38 NNM A1003 " pdb=" C39 NNM A1003 " ideal model delta sigma weight residual 1.332 1.544 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C13 NNM A1003 " pdb=" C14 NNM A1003 " ideal model delta sigma weight residual 1.332 1.541 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C28 NNM A1003 " pdb=" C29 NNM A1003 " ideal model delta sigma weight residual 1.332 1.541 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C23 NNM A1003 " pdb=" C24 NNM A1003 " ideal model delta sigma weight residual 1.332 1.537 -0.205 2.00e-02 2.50e+03 1.05e+02 ... (remaining 12070 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 16008 3.39 - 6.78: 312 6.78 - 10.17: 61 10.17 - 13.56: 3 13.56 - 16.95: 4 Bond angle restraints: 16388 Sorted by residual: angle pdb=" O3P CPL A1002 " pdb=" P CPL A1002 " pdb=" O4P CPL A1002 " ideal model delta sigma weight residual 93.29 110.24 -16.95 3.00e+00 1.11e-01 3.19e+01 angle pdb=" N ILE A 707 " pdb=" CA ILE A 707 " pdb=" C ILE A 707 " ideal model delta sigma weight residual 113.43 107.48 5.95 1.09e+00 8.42e-01 2.98e+01 angle pdb=" O3P CPL B1002 " pdb=" P CPL B1002 " pdb=" O4P CPL B1002 " ideal model delta sigma weight residual 93.29 109.45 -16.16 3.00e+00 1.11e-01 2.90e+01 angle pdb=" N VAL A 589 " pdb=" CA VAL A 589 " pdb=" C VAL A 589 " ideal model delta sigma weight residual 111.90 107.85 4.05 8.10e-01 1.52e+00 2.50e+01 angle pdb=" C16 NNM A1003 " pdb=" C17 NNM A1003 " pdb=" C18 NNM A1003 " ideal model delta sigma weight residual 112.52 126.99 -14.47 3.00e+00 1.11e-01 2.33e+01 ... (remaining 16383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 6823 35.34 - 70.68: 79 70.68 - 106.01: 12 106.01 - 141.35: 1 141.35 - 176.69: 1 Dihedral angle restraints: 6916 sinusoidal: 2774 harmonic: 4142 Sorted by residual: dihedral pdb=" CA PRO A 530 " pdb=" C PRO A 530 " pdb=" N ALA A 531 " pdb=" CA ALA A 531 " ideal model delta harmonic sigma weight residual 180.00 151.28 28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA GLY A 160 " pdb=" C GLY A 160 " pdb=" N VAL A 161 " pdb=" CA VAL A 161 " ideal model delta harmonic sigma weight residual 180.00 -152.98 -27.02 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA TRP B 583 " pdb=" C TRP B 583 " pdb=" N PRO B 584 " pdb=" CA PRO B 584 " ideal model delta harmonic sigma weight residual 180.00 156.62 23.38 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 6913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1143 0.048 - 0.097: 447 0.097 - 0.145: 115 0.145 - 0.193: 33 0.193 - 0.241: 8 Chirality restraints: 1746 Sorted by residual: chirality pdb=" CG LEU B 59 " pdb=" CB LEU B 59 " pdb=" CD1 LEU B 59 " pdb=" CD2 LEU B 59 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C2 CPL B1003 " pdb=" C1 CPL B1003 " pdb=" C3 CPL B1003 " pdb=" O2 CPL B1003 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE A 30 " pdb=" CA ILE A 30 " pdb=" CG1 ILE A 30 " pdb=" CG2 ILE A 30 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1743 not shown) Planarity restraints: 2029 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 727 " 0.036 2.00e-02 2.50e+03 2.32e-02 1.34e+01 pdb=" CG TRP A 727 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP A 727 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 727 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 727 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 727 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 727 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 727 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 727 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 727 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 654 " -0.057 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO B 655 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 655 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 655 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 590 " 0.026 2.00e-02 2.50e+03 1.91e-02 9.16e+00 pdb=" CG TRP A 590 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 590 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 590 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 590 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 590 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 590 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 590 " 0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 590 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 590 " -0.003 2.00e-02 2.50e+03 ... (remaining 2026 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2291 2.77 - 3.30: 10834 3.30 - 3.83: 20351 3.83 - 4.37: 24153 4.37 - 4.90: 41405 Nonbonded interactions: 99034 Sorted by model distance: nonbonded pdb=" OE2 GLU B 93 " pdb=" OH TYR B 142 " model vdw 2.236 3.040 nonbonded pdb=" O LEU A 151 " pdb=" OG1 THR A 155 " model vdw 2.249 3.040 nonbonded pdb=" O PHE A 139 " pdb=" OG SER A 143 " model vdw 2.259 3.040 nonbonded pdb=" O ASN B 191 " pdb=" OG1 THR B 195 " model vdw 2.267 3.040 nonbonded pdb=" O PRO B 68 " pdb=" OG1 THR B 72 " model vdw 2.280 3.040 ... (remaining 99029 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 11.550 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 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 0.230 12078 Z= 0.472 Angle : 1.163 16.952 16396 Z= 0.573 Chirality : 0.057 0.241 1746 Planarity : 0.008 0.086 2027 Dihedral : 12.491 176.689 4259 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.57 % Allowed : 5.01 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.56 (0.16), residues: 1413 helix: -3.27 (0.12), residues: 655 sheet: -3.24 (0.45), residues: 102 loop : -2.61 (0.19), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 27 TYR 0.042 0.003 TYR A 573 PHE 0.040 0.004 PHE B 301 TRP 0.061 0.003 TRP A 727 HIS 0.026 0.002 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.01023 / 0.47 (12075) covalent geometry : angle 1.16169 / 0.57 (16388) SS BOND : bond 0.00475 / 0.32 ( 1) SS BOND : angle 2.05886 / 1.17 ( 2) hydrogen bonds : bond 0.15158 / 10.51 ( 546) hydrogen bonds : angle 10.52114 / 7.41 ( 1566) link_NAG-ASN : bond 0.00107 / 0.07 ( 2) link_NAG-ASN : angle 3.23350 / 1.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 271 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 47 LEU cc_start: 0.8457 (tp) cc_final: 0.8178 (tp) REVERT: A 48 LYS cc_start: 0.8016 (ttpt) cc_final: 0.7783 (tttp) REVERT: A 148 THR cc_start: 0.8947 (t) cc_final: 0.8722 (m) REVERT: A 229 MET cc_start: 0.8397 (ttm) cc_final: 0.8011 (mtp) REVERT: A 264 LYS cc_start: 0.8139 (tmtp) cc_final: 0.7827 (tptp) REVERT: A 315 LYS cc_start: 0.8103 (mtpm) cc_final: 0.7898 (mmtp) REVERT: A 340 THR cc_start: 0.8859 (m) cc_final: 0.8533 (p) REVERT: A 364 TYR cc_start: 0.7322 (t80) cc_final: 0.6582 (t80) REVERT: A 370 ASN cc_start: 0.7506 (m-40) cc_final: 0.7159 (m-40) REVERT: A 398 ARG cc_start: 0.7176 (mtt180) cc_final: 0.6632 (mtt90) REVERT: A 407 ARG cc_start: 0.7645 (mmt90) cc_final: 0.7387 (mmt-90) REVERT: A 474 MET cc_start: 0.8288 (mmm) cc_final: 0.7889 (mtp) REVERT: A 525 ARG cc_start: 0.7974 (mmt90) cc_final: 0.7645 (mmt-90) REVERT: A 538 ILE cc_start: 0.8408 (mm) cc_final: 0.8191 (mt) REVERT: A 588 ILE cc_start: 0.8541 (tt) cc_final: 0.8275 (mt) REVERT: A 603 ILE cc_start: 0.7454 (tp) cc_final: 0.7035 (pt) REVERT: A 687 TYR cc_start: 0.8058 (m-10) cc_final: 0.7801 (m-80) REVERT: A 717 LEU cc_start: 0.7518 (tp) cc_final: 0.7007 (mt) REVERT: B 80 MET cc_start: 0.8218 (mpp) cc_final: 0.7852 (mtm) REVERT: B 219 MET cc_start: 0.8577 (mmt) cc_final: 0.8255 (mmt) REVERT: B 543 TYR cc_start: 0.6925 (m-80) cc_final: 0.6604 (m-80) REVERT: B 699 LYS cc_start: 0.7945 (mttt) cc_final: 0.7658 (mptt) REVERT: B 753 ILE cc_start: 0.8266 (tt) cc_final: 0.7426 (tt) outliers start: 7 outliers final: 4 residues processed: 276 average time/residue: 0.1191 time to fit residues: 46.3673 Evaluate side-chains 154 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 150 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 713 TRP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 611 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 50.0000 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 HIS ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN A 482 HIS A 546 HIS A 632 HIS A 719 GLN B 106 HIS B 110 HIS B 221 HIS B 308 HIS ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN B 633 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.173765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.123691 restraints weight = 14350.580| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.30 r_work: 0.2971 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12078 Z= 0.184 Angle : 0.666 9.980 16396 Z= 0.343 Chirality : 0.044 0.164 1746 Planarity : 0.006 0.065 2027 Dihedral : 11.623 178.093 1674 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.83 % Allowed : 10.42 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.19), residues: 1413 helix: -0.89 (0.18), residues: 654 sheet: -2.47 (0.56), residues: 78 loop : -2.32 (0.20), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 702 TYR 0.018 0.002 TYR A 734 PHE 0.024 0.002 PHE B 301 TRP 0.033 0.002 TRP A 727 HIS 0.012 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (12075) covalent geometry : angle 0.66437 / 0.34 (16388) SS BOND : bond 0.00151 / 0.10 ( 1) SS BOND : angle 0.90022 / 0.49 ( 2) hydrogen bonds : bond 0.04458 / 2.94 ( 546) hydrogen bonds : angle 5.89170 / 4.12 ( 1566) link_NAG-ASN : bond 0.00092 / 0.07 ( 2) link_NAG-ASN : angle 2.45276 / 1.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8545 (tp) cc_final: 0.8221 (mm) REVERT: A 264 LYS cc_start: 0.8555 (tmtp) cc_final: 0.8114 (tptp) REVERT: A 315 LYS cc_start: 0.8398 (mtpm) cc_final: 0.8001 (mmtp) REVERT: A 398 ARG cc_start: 0.6783 (mtt180) cc_final: 0.6058 (mtt90) REVERT: A 407 ARG cc_start: 0.7721 (mmt90) cc_final: 0.7503 (mmt-90) REVERT: A 444 VAL cc_start: 0.8552 (t) cc_final: 0.8269 (p) REVERT: A 447 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8566 (mp) REVERT: A 449 LYS cc_start: 0.8723 (mttt) cc_final: 0.8453 (mtmm) REVERT: A 459 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8199 (pm20) REVERT: A 474 MET cc_start: 0.8837 (mmm) cc_final: 0.8288 (mtp) REVERT: A 478 TYR cc_start: 0.7992 (m-80) cc_final: 0.7481 (m-10) REVERT: A 610 SER cc_start: 0.8958 (t) cc_final: 0.8569 (p) REVERT: A 619 LYS cc_start: 0.7883 (mmmm) cc_final: 0.7633 (mtpt) REVERT: A 622 LYS cc_start: 0.8991 (mttp) cc_final: 0.8745 (mtmm) REVERT: B 527 GLU cc_start: 0.7071 (tp30) cc_final: 0.6742 (tp30) REVERT: B 590 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8577 (tp) REVERT: B 672 VAL cc_start: 0.8881 (t) cc_final: 0.8361 (p) REVERT: B 699 LYS cc_start: 0.7876 (mttt) cc_final: 0.7664 (mptt) outliers start: 35 outliers final: 18 residues processed: 186 average time/residue: 0.1016 time to fit residues: 28.3303 Evaluate side-chains 152 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 713 TRP Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 637 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 108 optimal weight: 30.0000 chunk 104 optimal weight: 30.0000 chunk 122 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 111 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 HIS ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 HIS ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 741 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.171046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.112671 restraints weight = 14537.015| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.49 r_work: 0.2906 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12078 Z= 0.219 Angle : 0.661 10.073 16396 Z= 0.335 Chirality : 0.045 0.151 1746 Planarity : 0.005 0.056 2027 Dihedral : 11.110 176.431 1671 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.55 % Allowed : 10.58 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.21), residues: 1413 helix: 0.13 (0.19), residues: 657 sheet: -2.62 (0.51), residues: 89 loop : -2.09 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 64 TYR 0.019 0.002 TYR A 364 PHE 0.019 0.002 PHE B 301 TRP 0.032 0.002 TRP A 727 HIS 0.006 0.001 HIS B 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.22 (12075) covalent geometry : angle 0.65899 / 0.33 (16388) SS BOND : bond 0.00204 / 0.14 ( 1) SS BOND : angle 1.06239 / 0.59 ( 2) hydrogen bonds : bond 0.04328 / 2.84 ( 546) hydrogen bonds : angle 5.27753 / 3.67 ( 1566) link_NAG-ASN : bond 0.00119 / 0.08 ( 2) link_NAG-ASN : angle 3.00719 / 1.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 142 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8403 (tp) cc_final: 0.8165 (mm) REVERT: A 264 LYS cc_start: 0.8485 (tmtp) cc_final: 0.8069 (tptp) REVERT: A 315 LYS cc_start: 0.8163 (mtpm) cc_final: 0.7784 (mmtp) REVERT: A 364 TYR cc_start: 0.7581 (t80) cc_final: 0.6656 (t80) REVERT: A 368 ASP cc_start: 0.7214 (m-30) cc_final: 0.5885 (m-30) REVERT: A 398 ARG cc_start: 0.6727 (mtt180) cc_final: 0.5867 (mtt90) REVERT: A 442 ASP cc_start: 0.7660 (m-30) cc_final: 0.7035 (m-30) REVERT: A 449 LYS cc_start: 0.8708 (mttt) cc_final: 0.8439 (mtmt) REVERT: A 459 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8104 (pm20) REVERT: A 474 MET cc_start: 0.8871 (mmm) cc_final: 0.8204 (mtp) REVERT: A 478 TYR cc_start: 0.7968 (m-80) cc_final: 0.7355 (m-10) REVERT: A 576 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8027 (mm-30) REVERT: A 610 SER cc_start: 0.8906 (t) cc_final: 0.8578 (p) REVERT: A 619 LYS cc_start: 0.7867 (mmmm) cc_final: 0.7643 (mtpt) REVERT: A 622 LYS cc_start: 0.8862 (mttp) cc_final: 0.8623 (mtmm) REVERT: A 674 ILE cc_start: 0.8560 (mm) cc_final: 0.8308 (mt) REVERT: B 63 GLU cc_start: 0.5771 (mm-30) cc_final: 0.5482 (tm-30) REVERT: B 126 TYR cc_start: 0.8689 (t80) cc_final: 0.8482 (t80) REVERT: B 322 MET cc_start: 0.8752 (mmm) cc_final: 0.7977 (mmm) REVERT: B 527 GLU cc_start: 0.7142 (tp30) cc_final: 0.6439 (tp30) REVERT: B 590 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8626 (tp) REVERT: B 640 ARG cc_start: 0.8023 (mmt90) cc_final: 0.7806 (mmm160) REVERT: B 650 MET cc_start: 0.9000 (tpp) cc_final: 0.8727 (tpp) REVERT: B 656 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8440 (tp) REVERT: B 672 VAL cc_start: 0.8831 (t) cc_final: 0.8362 (p) REVERT: B 699 LYS cc_start: 0.7729 (mttt) cc_final: 0.7475 (mptt) REVERT: B 709 MET cc_start: 0.7248 (mmp) cc_final: 0.6953 (tpp) outliers start: 44 outliers final: 24 residues processed: 178 average time/residue: 0.0981 time to fit residues: 26.3537 Evaluate side-chains 157 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 546 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 713 TRP Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 656 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 30.0000 chunk 115 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN A 371 ASN A 546 HIS ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.171864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.120090 restraints weight = 14501.338| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.39 r_work: 0.2902 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12078 Z= 0.207 Angle : 0.638 10.174 16396 Z= 0.323 Chirality : 0.044 0.225 1746 Planarity : 0.005 0.055 2027 Dihedral : 10.862 175.462 1671 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.36 % Allowed : 11.31 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.22), residues: 1413 helix: 0.61 (0.20), residues: 656 sheet: -2.38 (0.50), residues: 93 loop : -1.90 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 407 TYR 0.016 0.002 TYR A 641 PHE 0.016 0.002 PHE A 537 TRP 0.028 0.001 TRP A 727 HIS 0.007 0.001 HIS A 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.21 (12075) covalent geometry : angle 0.63521 / 0.32 (16388) SS BOND : bond 0.00228 / 0.15 ( 1) SS BOND : angle 0.93854 / 0.52 ( 2) hydrogen bonds : bond 0.04204 / 2.74 ( 546) hydrogen bonds : angle 5.00946 / 3.47 ( 1566) link_NAG-ASN : bond 0.00090 / 0.06 ( 2) link_NAG-ASN : angle 2.96557 / 1.59 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 132 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8515 (tp) cc_final: 0.8295 (mm) REVERT: A 264 LYS cc_start: 0.8526 (tmtp) cc_final: 0.8129 (tptp) REVERT: A 315 LYS cc_start: 0.8223 (mtpm) cc_final: 0.7851 (mmtp) REVERT: A 364 TYR cc_start: 0.7665 (t80) cc_final: 0.6779 (t80) REVERT: A 398 ARG cc_start: 0.6712 (mtt180) cc_final: 0.5884 (mtt90) REVERT: A 407 ARG cc_start: 0.7340 (mmt-90) cc_final: 0.7001 (mpt180) REVERT: A 442 ASP cc_start: 0.7645 (m-30) cc_final: 0.7125 (m-30) REVERT: A 449 LYS cc_start: 0.8762 (mttt) cc_final: 0.8527 (mtmt) REVERT: A 459 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8070 (pm20) REVERT: A 474 MET cc_start: 0.8809 (mmm) cc_final: 0.8227 (mtp) REVERT: A 478 TYR cc_start: 0.8077 (m-80) cc_final: 0.7472 (m-10) REVERT: A 610 SER cc_start: 0.8959 (t) cc_final: 0.8624 (p) REVERT: A 619 LYS cc_start: 0.7890 (mmmm) cc_final: 0.7677 (mtpt) REVERT: B 63 GLU cc_start: 0.5906 (mm-30) cc_final: 0.5579 (tm-30) REVERT: B 126 TYR cc_start: 0.8737 (t80) cc_final: 0.8532 (t80) REVERT: B 322 MET cc_start: 0.8888 (mmm) cc_final: 0.8122 (mmm) REVERT: B 344 LEU cc_start: -0.0390 (OUTLIER) cc_final: -0.0652 (tt) REVERT: B 527 GLU cc_start: 0.7180 (tp30) cc_final: 0.6503 (tp30) REVERT: B 559 MET cc_start: 0.7949 (mtp) cc_final: 0.7686 (mtt) REVERT: B 605 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8397 (pt) REVERT: B 640 ARG cc_start: 0.8072 (mmt90) cc_final: 0.7856 (mmm160) REVERT: B 650 MET cc_start: 0.9138 (tpp) cc_final: 0.8538 (tpp) REVERT: B 656 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8515 (tp) REVERT: B 672 VAL cc_start: 0.8903 (t) cc_final: 0.8434 (p) outliers start: 54 outliers final: 26 residues processed: 174 average time/residue: 0.0958 time to fit residues: 25.5174 Evaluate side-chains 152 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 656 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 108 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 119 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN A 546 HIS B 362 HIS ** B 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.172871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.122783 restraints weight = 14572.466| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.51 r_work: 0.3052 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12078 Z= 0.142 Angle : 0.587 9.717 16396 Z= 0.298 Chirality : 0.042 0.170 1746 Planarity : 0.004 0.053 2027 Dihedral : 10.502 175.548 1669 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.31 % Allowed : 12.76 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.22), residues: 1413 helix: 0.99 (0.20), residues: 649 sheet: -2.24 (0.50), residues: 95 loop : -1.68 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 407 TYR 0.015 0.001 TYR A 364 PHE 0.013 0.001 PHE A 537 TRP 0.021 0.001 TRP A 727 HIS 0.006 0.001 HIS A 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (12075) covalent geometry : angle 0.58417 / 0.30 (16388) SS BOND : bond 0.00251 / 0.17 ( 1) SS BOND : angle 0.72615 / 0.40 ( 2) hydrogen bonds : bond 0.03923 / 2.56 ( 546) hydrogen bonds : angle 4.70993 / 3.26 ( 1566) link_NAG-ASN : bond 0.00141 / 0.10 ( 2) link_NAG-ASN : angle 2.97550 / 1.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.8582 (tmtp) cc_final: 0.8216 (tptp) REVERT: A 315 LYS cc_start: 0.8311 (mtpm) cc_final: 0.7966 (mmtp) REVERT: A 364 TYR cc_start: 0.7505 (t80) cc_final: 0.6750 (t80) REVERT: A 368 ASP cc_start: 0.7344 (m-30) cc_final: 0.5733 (m-30) REVERT: A 398 ARG cc_start: 0.6782 (mtt180) cc_final: 0.5907 (mtt90) REVERT: A 407 ARG cc_start: 0.7333 (mmt-90) cc_final: 0.7005 (mpt180) REVERT: A 442 ASP cc_start: 0.7540 (m-30) cc_final: 0.6905 (m-30) REVERT: A 449 LYS cc_start: 0.8740 (mttt) cc_final: 0.8527 (mtmt) REVERT: A 459 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8103 (pm20) REVERT: A 474 MET cc_start: 0.8604 (mmm) cc_final: 0.8042 (mtp) REVERT: A 478 TYR cc_start: 0.7964 (m-80) cc_final: 0.7424 (m-10) REVERT: A 610 SER cc_start: 0.8880 (t) cc_final: 0.8639 (p) REVERT: B 63 GLU cc_start: 0.6038 (mm-30) cc_final: 0.5820 (tm-30) REVERT: B 322 MET cc_start: 0.8896 (mmm) cc_final: 0.8201 (mmm) REVERT: B 344 LEU cc_start: -0.0163 (OUTLIER) cc_final: -0.0431 (tt) REVERT: B 527 GLU cc_start: 0.7167 (tp30) cc_final: 0.6511 (tp30) REVERT: B 571 ASP cc_start: 0.8160 (m-30) cc_final: 0.7715 (m-30) REVERT: B 605 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8305 (pt) REVERT: B 656 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8519 (tp) REVERT: B 672 VAL cc_start: 0.8829 (t) cc_final: 0.8417 (p) outliers start: 41 outliers final: 22 residues processed: 170 average time/residue: 0.1024 time to fit residues: 26.2746 Evaluate side-chains 156 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 656 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 115 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 125 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 HIS A 359 GLN A 370 ASN A 546 HIS ** B 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.169529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.118290 restraints weight = 14589.981| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.35 r_work: 0.3009 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12078 Z= 0.208 Angle : 0.621 10.186 16396 Z= 0.314 Chirality : 0.044 0.182 1746 Planarity : 0.004 0.055 2027 Dihedral : 10.461 173.399 1669 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.12 % Allowed : 12.76 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.22), residues: 1413 helix: 1.08 (0.20), residues: 643 sheet: -2.07 (0.57), residues: 76 loop : -1.56 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 336 TYR 0.016 0.002 TYR A 364 PHE 0.015 0.002 PHE A 121 TRP 0.026 0.001 TRP A 727 HIS 0.007 0.001 HIS B 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 (12075) covalent geometry : angle 0.61937 / 0.31 (16388) SS BOND : bond 0.00245 / 0.16 ( 1) SS BOND : angle 0.85089 / 0.47 ( 2) hydrogen bonds : bond 0.04106 / 2.68 ( 546) hydrogen bonds : angle 4.70603 / 3.26 ( 1566) link_NAG-ASN : bond 0.00060 / 0.04 ( 2) link_NAG-ASN : angle 2.66455 / 1.51 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 130 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 264 LYS cc_start: 0.8764 (tmtp) cc_final: 0.8345 (tptp) REVERT: A 315 LYS cc_start: 0.8358 (mtpm) cc_final: 0.8009 (mmtp) REVERT: A 364 TYR cc_start: 0.7664 (t80) cc_final: 0.6911 (t80) REVERT: A 368 ASP cc_start: 0.7450 (m-30) cc_final: 0.5956 (m-30) REVERT: A 398 ARG cc_start: 0.6875 (mtt180) cc_final: 0.6091 (mtt90) REVERT: A 407 ARG cc_start: 0.7521 (mmt-90) cc_final: 0.7228 (mpt180) REVERT: A 442 ASP cc_start: 0.7717 (m-30) cc_final: 0.6932 (m-30) REVERT: A 449 LYS cc_start: 0.8775 (mttt) cc_final: 0.8568 (mtmt) REVERT: A 459 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8189 (pm20) REVERT: A 474 MET cc_start: 0.8682 (mmm) cc_final: 0.8108 (mtp) REVERT: A 478 TYR cc_start: 0.8210 (m-80) cc_final: 0.7671 (m-10) REVERT: A 610 SER cc_start: 0.8968 (t) cc_final: 0.8690 (p) REVERT: B 63 GLU cc_start: 0.6221 (mm-30) cc_final: 0.5837 (tm-30) REVERT: B 322 MET cc_start: 0.8945 (mmm) cc_final: 0.8250 (mmm) REVERT: B 527 GLU cc_start: 0.7261 (tp30) cc_final: 0.6676 (tp30) REVERT: B 571 ASP cc_start: 0.8249 (m-30) cc_final: 0.7815 (m-30) REVERT: B 605 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8497 (pt) REVERT: B 656 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8578 (tp) REVERT: B 672 VAL cc_start: 0.9057 (t) cc_final: 0.8605 (p) outliers start: 51 outliers final: 31 residues processed: 167 average time/residue: 0.0960 time to fit residues: 24.4726 Evaluate side-chains 161 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 712 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 20.0000 chunk 65 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 HIS A 546 HIS ** B 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.173177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.122499 restraints weight = 14610.913| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.32 r_work: 0.2953 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12078 Z= 0.128 Angle : 0.567 9.802 16396 Z= 0.286 Chirality : 0.042 0.154 1746 Planarity : 0.004 0.052 2027 Dihedral : 10.148 173.934 1669 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.47 % Allowed : 14.05 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.22), residues: 1413 helix: 1.28 (0.20), residues: 650 sheet: -2.01 (0.49), residues: 98 loop : -1.44 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 336 TYR 0.015 0.001 TYR A 364 PHE 0.013 0.001 PHE A 537 TRP 0.017 0.001 TRP A 727 HIS 0.005 0.001 HIS A 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (12075) covalent geometry : angle 0.56369 / 0.29 (16388) SS BOND : bond 0.00202 / 0.13 ( 1) SS BOND : angle 0.66670 / 0.37 ( 2) hydrogen bonds : bond 0.03745 / 2.44 ( 546) hydrogen bonds : angle 4.44953 / 3.08 ( 1566) link_NAG-ASN : bond 0.00381 / 0.26 ( 2) link_NAG-ASN : angle 3.24138 / 1.57 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 135 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.8646 (tmtp) cc_final: 0.8257 (tptp) REVERT: A 315 LYS cc_start: 0.8271 (mtpm) cc_final: 0.7886 (mmtp) REVERT: A 364 TYR cc_start: 0.7413 (t80) cc_final: 0.6709 (t80) REVERT: A 368 ASP cc_start: 0.7248 (m-30) cc_final: 0.5797 (m-30) REVERT: A 370 ASN cc_start: 0.7548 (m-40) cc_final: 0.7257 (m-40) REVERT: A 398 ARG cc_start: 0.6544 (mtt180) cc_final: 0.5801 (mtt90) REVERT: A 407 ARG cc_start: 0.7283 (mmt-90) cc_final: 0.7049 (mpt180) REVERT: A 442 ASP cc_start: 0.7442 (m-30) cc_final: 0.6400 (m-30) REVERT: A 449 LYS cc_start: 0.8752 (mttt) cc_final: 0.8523 (mtmt) REVERT: A 459 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8196 (pm20) REVERT: A 474 MET cc_start: 0.8739 (mmm) cc_final: 0.8132 (mtp) REVERT: A 478 TYR cc_start: 0.7843 (m-80) cc_final: 0.7266 (m-10) REVERT: A 495 GLU cc_start: 0.7805 (pp20) cc_final: 0.7387 (pp20) REVERT: A 610 SER cc_start: 0.8845 (t) cc_final: 0.8582 (p) REVERT: B 63 GLU cc_start: 0.6086 (mm-30) cc_final: 0.5690 (tm-30) REVERT: B 322 MET cc_start: 0.8919 (mmm) cc_final: 0.8151 (mmm) REVERT: B 527 GLU cc_start: 0.7341 (tp30) cc_final: 0.6732 (tp30) REVERT: B 543 TYR cc_start: 0.6962 (m-80) cc_final: 0.6697 (m-80) REVERT: B 571 ASP cc_start: 0.8221 (m-30) cc_final: 0.7754 (m-30) REVERT: B 605 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8306 (pt) REVERT: B 650 MET cc_start: 0.9247 (tpp) cc_final: 0.8905 (tpp) REVERT: B 656 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8508 (tp) REVERT: B 672 VAL cc_start: 0.8879 (t) cc_final: 0.8420 (p) REVERT: B 735 MET cc_start: 0.8556 (mtt) cc_final: 0.8276 (mtm) outliers start: 43 outliers final: 25 residues processed: 168 average time/residue: 0.0931 time to fit residues: 24.1954 Evaluate side-chains 153 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 656 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 18 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 101 optimal weight: 30.0000 chunk 63 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 HIS B 386 ASN ** B 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.170888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.120267 restraints weight = 14534.003| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.38 r_work: 0.2907 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12078 Z= 0.178 Angle : 0.607 10.415 16396 Z= 0.303 Chirality : 0.043 0.206 1746 Planarity : 0.004 0.053 2027 Dihedral : 10.131 172.222 1669 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.47 % Allowed : 14.62 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.22), residues: 1413 helix: 1.30 (0.20), residues: 645 sheet: -1.89 (0.50), residues: 98 loop : -1.37 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 336 TYR 0.014 0.001 TYR A 641 PHE 0.014 0.002 PHE A 537 TRP 0.022 0.001 TRP A 727 HIS 0.005 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (12075) covalent geometry : angle 0.60453 / 0.30 (16388) SS BOND : bond 0.00193 / 0.13 ( 1) SS BOND : angle 0.72314 / 0.40 ( 2) hydrogen bonds : bond 0.03933 / 2.57 ( 546) hydrogen bonds : angle 4.47842 / 3.11 ( 1566) link_NAG-ASN : bond 0.00082 / 0.06 ( 2) link_NAG-ASN : angle 2.93966 / 1.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 127 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 47 LEU cc_start: 0.8472 (tp) cc_final: 0.8234 (tp) REVERT: A 264 LYS cc_start: 0.8687 (tmtp) cc_final: 0.8308 (tptp) REVERT: A 315 LYS cc_start: 0.8255 (mtpm) cc_final: 0.7878 (mmtp) REVERT: A 364 TYR cc_start: 0.7476 (t80) cc_final: 0.6741 (t80) REVERT: A 368 ASP cc_start: 0.7246 (m-30) cc_final: 0.5782 (m-30) REVERT: A 370 ASN cc_start: 0.7610 (m-40) cc_final: 0.7314 (m-40) REVERT: A 398 ARG cc_start: 0.6517 (mtt180) cc_final: 0.5797 (mtt90) REVERT: A 407 ARG cc_start: 0.7275 (mmt-90) cc_final: 0.7021 (mpt180) REVERT: A 442 ASP cc_start: 0.7306 (m-30) cc_final: 0.6394 (m-30) REVERT: A 449 LYS cc_start: 0.8709 (mttt) cc_final: 0.8479 (mtmt) REVERT: A 459 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8128 (pm20) REVERT: A 474 MET cc_start: 0.8553 (mmm) cc_final: 0.8126 (mtp) REVERT: A 478 TYR cc_start: 0.7908 (m-80) cc_final: 0.7313 (m-10) REVERT: A 495 GLU cc_start: 0.7810 (pp20) cc_final: 0.7397 (pp20) REVERT: A 610 SER cc_start: 0.8874 (t) cc_final: 0.8600 (m) REVERT: B 63 GLU cc_start: 0.6091 (mm-30) cc_final: 0.5686 (tm-30) REVERT: B 322 MET cc_start: 0.8924 (mmm) cc_final: 0.8177 (mmm) REVERT: B 527 GLU cc_start: 0.7320 (tp30) cc_final: 0.6731 (tp30) REVERT: B 543 TYR cc_start: 0.6967 (m-80) cc_final: 0.6712 (m-80) REVERT: B 571 ASP cc_start: 0.8230 (m-30) cc_final: 0.7761 (m-30) REVERT: B 605 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8380 (pt) REVERT: B 650 MET cc_start: 0.9288 (tpp) cc_final: 0.8912 (tpp) REVERT: B 656 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8526 (tp) REVERT: B 672 VAL cc_start: 0.8963 (t) cc_final: 0.8506 (p) outliers start: 43 outliers final: 26 residues processed: 159 average time/residue: 0.0924 time to fit residues: 22.7323 Evaluate side-chains 152 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 546 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 656 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 95 optimal weight: 2.9990 chunk 81 optimal weight: 0.0770 chunk 76 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 110 optimal weight: 50.0000 chunk 51 optimal weight: 3.9990 chunk 103 optimal weight: 30.0000 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 HIS ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.168898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.117620 restraints weight = 14437.071| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.32 r_work: 0.2870 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 12078 Z= 0.229 Angle : 0.637 10.376 16396 Z= 0.318 Chirality : 0.045 0.229 1746 Planarity : 0.004 0.055 2027 Dihedral : 10.187 174.962 1669 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.99 % Allowed : 15.02 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.28 (0.22), residues: 1413 helix: 1.17 (0.20), residues: 647 sheet: -1.84 (0.50), residues: 98 loop : -1.30 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 336 TYR 0.015 0.002 TYR A 641 PHE 0.016 0.002 PHE A 121 TRP 0.026 0.001 TRP A 727 HIS 0.019 0.001 HIS A 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.23 (12075) covalent geometry : angle 0.63520 / 0.32 (16388) SS BOND : bond 0.00208 / 0.14 ( 1) SS BOND : angle 0.78235 / 0.44 ( 2) hydrogen bonds : bond 0.04095 / 2.68 ( 546) hydrogen bonds : angle 4.56606 / 3.17 ( 1566) link_NAG-ASN : bond 0.00081 / 0.05 ( 2) link_NAG-ASN : angle 2.86136 / 1.57 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.8688 (tmtp) cc_final: 0.8265 (tptp) REVERT: A 315 LYS cc_start: 0.8239 (mtpm) cc_final: 0.7862 (mmtp) REVERT: A 364 TYR cc_start: 0.7512 (t80) cc_final: 0.6706 (t80) REVERT: A 368 ASP cc_start: 0.7241 (m-30) cc_final: 0.5821 (m-30) REVERT: A 370 ASN cc_start: 0.7704 (m-40) cc_final: 0.7443 (m-40) REVERT: A 398 ARG cc_start: 0.6612 (mtt180) cc_final: 0.5864 (mtt90) REVERT: A 407 ARG cc_start: 0.7295 (mmt-90) cc_final: 0.7027 (mpt180) REVERT: A 442 ASP cc_start: 0.7319 (m-30) cc_final: 0.6481 (m-30) REVERT: A 449 LYS cc_start: 0.8716 (mttt) cc_final: 0.8489 (mtmt) REVERT: A 459 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8110 (pm20) REVERT: A 474 MET cc_start: 0.8511 (mmm) cc_final: 0.8105 (mtp) REVERT: A 478 TYR cc_start: 0.7968 (m-80) cc_final: 0.7393 (m-10) REVERT: A 495 GLU cc_start: 0.7805 (pp20) cc_final: 0.7411 (pp20) REVERT: A 546 HIS cc_start: 0.8234 (OUTLIER) cc_final: 0.6961 (m-70) REVERT: A 610 SER cc_start: 0.8923 (t) cc_final: 0.8631 (m) REVERT: B 63 GLU cc_start: 0.6088 (mm-30) cc_final: 0.5667 (tm-30) REVERT: B 93 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8234 (tt0) REVERT: B 322 MET cc_start: 0.8914 (mmm) cc_final: 0.8193 (mmm) REVERT: B 527 GLU cc_start: 0.7330 (tp30) cc_final: 0.6778 (tp30) REVERT: B 543 TYR cc_start: 0.6974 (m-80) cc_final: 0.6726 (m-80) REVERT: B 571 ASP cc_start: 0.8291 (m-30) cc_final: 0.7826 (m-30) REVERT: B 605 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8514 (pt) REVERT: B 656 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8514 (tp) REVERT: B 672 VAL cc_start: 0.8993 (t) cc_final: 0.8546 (p) outliers start: 37 outliers final: 26 residues processed: 149 average time/residue: 0.0958 time to fit residues: 21.8782 Evaluate side-chains 152 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 546 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 656 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 30.0000 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 HIS ** B 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.170752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.120106 restraints weight = 14529.402| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.57 r_work: 0.2857 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12078 Z= 0.143 Angle : 0.598 9.961 16396 Z= 0.297 Chirality : 0.042 0.188 1746 Planarity : 0.004 0.053 2027 Dihedral : 10.000 176.519 1669 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.67 % Allowed : 15.35 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.14 (0.22), residues: 1413 helix: 1.30 (0.20), residues: 649 sheet: -1.86 (0.51), residues: 92 loop : -1.23 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 336 TYR 0.015 0.001 TYR A 641 PHE 0.014 0.001 PHE B 552 TRP 0.020 0.001 TRP A 727 HIS 0.018 0.001 HIS A 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (12075) covalent geometry : angle 0.59556 / 0.30 (16388) SS BOND : bond 0.00180 / 0.12 ( 1) SS BOND : angle 0.66045 / 0.37 ( 2) hydrogen bonds : bond 0.03890 / 2.54 ( 546) hydrogen bonds : angle 4.44068 / 3.08 ( 1566) link_NAG-ASN : bond 0.00217 / 0.15 ( 2) link_NAG-ASN : angle 2.63852 / 1.44 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 0.416 Fit side-chains REVERT: A 264 LYS cc_start: 0.8658 (tmtp) cc_final: 0.8245 (tptp) REVERT: A 315 LYS cc_start: 0.8193 (mtpm) cc_final: 0.7824 (mmtp) REVERT: A 364 TYR cc_start: 0.7340 (t80) cc_final: 0.6632 (t80) REVERT: A 368 ASP cc_start: 0.7216 (m-30) cc_final: 0.5720 (m-30) REVERT: A 370 ASN cc_start: 0.7624 (m-40) cc_final: 0.7361 (m-40) REVERT: A 398 ARG cc_start: 0.6506 (mtt180) cc_final: 0.5767 (mtt90) REVERT: A 407 ARG cc_start: 0.7169 (mmt-90) cc_final: 0.6926 (mpt180) REVERT: A 442 ASP cc_start: 0.7144 (m-30) cc_final: 0.6313 (m-30) REVERT: A 449 LYS cc_start: 0.8765 (mttt) cc_final: 0.8537 (mtmt) REVERT: A 459 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8067 (pm20) REVERT: A 474 MET cc_start: 0.8452 (mmm) cc_final: 0.8004 (mtp) REVERT: A 478 TYR cc_start: 0.7749 (m-80) cc_final: 0.7175 (m-10) REVERT: A 495 GLU cc_start: 0.7717 (pp20) cc_final: 0.7335 (pp20) REVERT: A 546 HIS cc_start: 0.8006 (OUTLIER) cc_final: 0.6871 (m-70) REVERT: A 610 SER cc_start: 0.8850 (t) cc_final: 0.8601 (m) REVERT: A 734 TYR cc_start: 0.8360 (m-80) cc_final: 0.8159 (m-80) REVERT: B 63 GLU cc_start: 0.6077 (mm-30) cc_final: 0.5690 (tm-30) REVERT: B 322 MET cc_start: 0.8919 (mmm) cc_final: 0.8156 (mmm) REVERT: B 527 GLU cc_start: 0.7306 (tp30) cc_final: 0.6716 (tp30) REVERT: B 571 ASP cc_start: 0.8122 (m-30) cc_final: 0.7647 (m-30) REVERT: B 656 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8479 (tp) REVERT: B 672 VAL cc_start: 0.8872 (t) cc_final: 0.8459 (p) outliers start: 33 outliers final: 27 residues processed: 149 average time/residue: 0.0940 time to fit residues: 21.5227 Evaluate side-chains 150 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 546 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 709 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 92 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 104 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 HIS A 359 GLN A 360 GLN B 191 ASN ** B 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.173739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.121654 restraints weight = 14235.354| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.35 r_work: 0.2917 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12078 Z= 0.143 Angle : 0.601 11.831 16396 Z= 0.297 Chirality : 0.042 0.186 1746 Planarity : 0.004 0.053 2027 Dihedral : 9.875 177.131 1669 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.34 % Allowed : 16.24 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.22), residues: 1413 helix: 1.36 (0.20), residues: 648 sheet: -1.86 (0.51), residues: 92 loop : -1.17 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 336 TYR 0.016 0.001 TYR A 364 PHE 0.013 0.001 PHE B 552 TRP 0.019 0.001 TRP A 727 HIS 0.019 0.001 HIS A 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (12075) covalent geometry : angle 0.59627 / 0.30 (16388) SS BOND : bond 0.00197 / 0.13 ( 1) SS BOND : angle 0.68304 / 0.38 ( 2) hydrogen bonds : bond 0.03853 / 2.51 ( 546) hydrogen bonds : angle 4.40870 / 3.05 ( 1566) link_NAG-ASN : bond 0.00271 / 0.18 ( 2) link_NAG-ASN : angle 3.97932 / 2.04 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3119.53 seconds wall clock time: 54 minutes 34.87 seconds (3274.87 seconds total)