Starting phenix.real_space_refine on Fri Jul 3 06:38:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o1n_70013/07_2026/9o1n_70013.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o1n_70013/07_2026/9o1n_70013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o1n_70013/07_2026/9o1n_70013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o1n_70013/07_2026/9o1n_70013.map" model { file = "/net/cci-nas-00/data/ceres_data/9o1n_70013/07_2026/9o1n_70013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o1n_70013/07_2026/9o1n_70013.cif" } resolution = 3.56 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= 0.002 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 78 5.16 5 C 8048 2.51 5 N 2002 2.21 5 O 2168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12302 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 6148 Classifications: {'peptide': 750} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 33, 'TRANS': 716} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Restraints were copied for chains: B Time building chain proxies: 6.46, per 1000 atoms: 0.53 Number of scatterers: 12302 At special positions: 0 Unit cell: (81.675, 134.475, 114.675, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 78 16.00 O 2168 8.00 N 2002 7.00 C 8048 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 584.3 milliseconds 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 14 sheets defined 63.1% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 87 through 108 removed outlier: 4.312A pdb=" N ASN A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 143 Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 205 through 218 Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 264 through 273 removed outlier: 3.523A pdb=" N LEU A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 removed outlier: 4.120A pdb=" N ILE A 279 " --> pdb=" O PRO A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 293 Processing helix chain 'A' and resid 293 through 327 removed outlier: 3.814A pdb=" N TYR A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA A 313 " --> pdb=" O MET A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 3.677A pdb=" N LYS A 335 " --> pdb=" O CYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 376 removed outlier: 3.652A pdb=" N LYS A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 408 removed outlier: 4.090A pdb=" N THR A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 427 Processing helix chain 'A' and resid 450 through 482 removed outlier: 3.701A pdb=" N THR A 454 " --> pdb=" O CYS A 450 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 539 Processing helix chain 'A' and resid 544 through 573 removed outlier: 4.087A pdb=" N VAL A 561 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 565 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 614 removed outlier: 3.735A pdb=" N GLU A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 641 Proline residue: A 628 - end of helix Processing helix chain 'A' and resid 648 through 656 removed outlier: 3.607A pdb=" N HIS A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 656 " --> pdb=" O GLN A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 681 removed outlier: 4.060A pdb=" N TYR A 666 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU A 667 " --> pdb=" O GLY A 663 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET A 671 " --> pdb=" O GLU A 667 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN A 674 " --> pdb=" O GLU A 670 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 685 Processing helix chain 'A' and resid 687 through 710 removed outlier: 3.660A pdb=" N LEU A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 747 removed outlier: 3.841A pdb=" N VAL A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 759 removed outlier: 3.512A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 781 Processing helix chain 'A' and resid 825 through 857 Processing helix chain 'A' and resid 861 through 875 removed outlier: 3.805A pdb=" N GLU A 871 " --> pdb=" O LYS A 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 108 removed outlier: 4.312A pdb=" N ASN B 91 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN B 94 " --> pdb=" O THR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 143 Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'B' and resid 205 through 218 Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 264 through 273 removed outlier: 3.524A pdb=" N LEU B 268 " --> pdb=" O SER B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 279 removed outlier: 4.120A pdb=" N ILE B 279 " --> pdb=" O PRO B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 293 through 327 removed outlier: 3.814A pdb=" N TYR B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA B 313 " --> pdb=" O MET B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 339 removed outlier: 3.677A pdb=" N LYS B 335 " --> pdb=" O CYS B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 376 removed outlier: 3.652A pdb=" N LYS B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 408 removed outlier: 4.090A pdb=" N THR B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 427 Processing helix chain 'B' and resid 450 through 482 removed outlier: 3.702A pdb=" N THR B 454 " --> pdb=" O CYS B 450 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR B 477 " --> pdb=" O GLY B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 539 Processing helix chain 'B' and resid 544 through 573 removed outlier: 4.086A pdb=" N VAL B 561 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN B 562 " --> pdb=" O PHE B 558 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 565 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 614 removed outlier: 3.735A pdb=" N GLU B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 641 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 648 through 656 removed outlier: 3.607A pdb=" N HIS B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 681 removed outlier: 4.059A pdb=" N TYR B 666 " --> pdb=" O LEU B 662 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU B 667 " --> pdb=" O GLY B 663 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET B 671 " --> pdb=" O GLU B 667 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN B 674 " --> pdb=" O GLU B 670 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 685 Processing helix chain 'B' and resid 687 through 710 removed outlier: 3.660A pdb=" N LEU B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 747 removed outlier: 3.841A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 759 removed outlier: 3.511A pdb=" N ARG B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 875 removed outlier: 3.805A pdb=" N GLU B 871 " --> pdb=" O LYS B 867 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 115 removed outlier: 3.876A pdb=" N PHE A 73 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A 244 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N GLU A 78 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N TYR A 242 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 225 removed outlier: 3.665A pdb=" N GLN A 223 " --> pdb=" O LYS A 230 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 348 Processing sheet with id=AA5, first strand: chain 'A' and resid 430 through 432 Processing sheet with id=AA6, first strand: chain 'A' and resid 657 through 658 removed outlier: 7.628A pdb=" N GLN A 657 " --> pdb=" O ARG A 712 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 782 through 784 Processing sheet with id=AA8, first strand: chain 'B' and resid 111 through 115 removed outlier: 3.876A pdb=" N PHE B 73 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA B 244 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N GLU B 78 " --> pdb=" O TYR B 242 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N TYR B 242 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AB1, first strand: chain 'B' and resid 223 through 225 removed outlier: 3.666A pdb=" N GLN B 223 " --> pdb=" O LYS B 230 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 347 through 348 Processing sheet with id=AB3, first strand: chain 'B' and resid 430 through 432 Processing sheet with id=AB4, first strand: chain 'B' and resid 657 through 658 removed outlier: 7.628A pdb=" N GLN B 657 " --> pdb=" O ARG B 712 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 782 through 784 720 hydrogen bonds defined for protein. 2106 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.08 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3798 1.35 - 1.47: 3270 1.47 - 1.58: 5442 1.58 - 1.70: 0 1.70 - 1.82: 118 Bond restraints: 12628 Sorted by residual: bond pdb=" CB PRO A 816 " pdb=" CG PRO A 816 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.58e+00 bond pdb=" CB PRO B 816 " pdb=" CG PRO B 816 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.56e+00 bond pdb=" CG LEU B 105 " pdb=" CD2 LEU B 105 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 bond pdb=" CG LEU A 105 " pdb=" CD2 LEU A 105 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.17e+00 bond pdb=" CB ILE B 839 " pdb=" CG2 ILE B 839 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.07e+00 ... (remaining 12623 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 16945 2.46 - 4.92: 153 4.92 - 7.37: 20 7.37 - 9.83: 8 9.83 - 12.29: 6 Bond angle restraints: 17132 Sorted by residual: angle pdb=" CA PRO A 816 " pdb=" N PRO A 816 " pdb=" CD PRO A 816 " ideal model delta sigma weight residual 112.00 106.63 5.37 1.40e+00 5.10e-01 1.47e+01 angle pdb=" CA PRO B 816 " pdb=" N PRO B 816 " pdb=" CD PRO B 816 " ideal model delta sigma weight residual 112.00 106.64 5.36 1.40e+00 5.10e-01 1.47e+01 angle pdb=" CA LEU B 466 " pdb=" CB LEU B 466 " pdb=" CG LEU B 466 " ideal model delta sigma weight residual 116.30 128.59 -12.29 3.50e+00 8.16e-02 1.23e+01 angle pdb=" CA LEU A 466 " pdb=" CB LEU A 466 " pdb=" CG LEU A 466 " ideal model delta sigma weight residual 116.30 128.53 -12.23 3.50e+00 8.16e-02 1.22e+01 angle pdb=" CA LEU B 662 " pdb=" CB LEU B 662 " pdb=" CG LEU B 662 " ideal model delta sigma weight residual 116.30 127.87 -11.57 3.50e+00 8.16e-02 1.09e+01 ... (remaining 17127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 6484 17.44 - 34.89: 776 34.89 - 52.33: 182 52.33 - 69.78: 30 69.78 - 87.22: 20 Dihedral angle restraints: 7492 sinusoidal: 3044 harmonic: 4448 Sorted by residual: dihedral pdb=" CA TRP A 408 " pdb=" C TRP A 408 " pdb=" N ASP A 409 " pdb=" CA ASP A 409 " ideal model delta harmonic sigma weight residual 180.00 163.47 16.53 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA TRP B 408 " pdb=" C TRP B 408 " pdb=" N ASP B 409 " pdb=" CA ASP B 409 " ideal model delta harmonic sigma weight residual 180.00 163.50 16.50 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ASP B 583 " pdb=" CB ASP B 583 " pdb=" CG ASP B 583 " pdb=" OD1 ASP B 583 " ideal model delta sinusoidal sigma weight residual -30.00 -86.76 56.76 1 2.00e+01 2.50e-03 1.08e+01 ... (remaining 7489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1430 0.046 - 0.091: 367 0.091 - 0.137: 69 0.137 - 0.182: 6 0.182 - 0.228: 2 Chirality restraints: 1874 Sorted by residual: chirality pdb=" CG LEU A 236 " pdb=" CB LEU A 236 " pdb=" CD1 LEU A 236 " pdb=" CD2 LEU A 236 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CG LEU B 236 " pdb=" CB LEU B 236 " pdb=" CD1 LEU B 236 " pdb=" CD2 LEU B 236 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ILE B 646 " pdb=" N ILE B 646 " pdb=" C ILE B 646 " pdb=" CB ILE B 646 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.76e-01 ... (remaining 1871 not shown) Planarity restraints: 2142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 815 " -0.059 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO B 816 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 816 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 816 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 815 " -0.059 5.00e-02 4.00e+02 8.64e-02 1.20e+01 pdb=" N PRO A 816 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO A 816 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 816 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 763 " -0.038 5.00e-02 4.00e+02 5.68e-02 5.17e+00 pdb=" N PRO B 764 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 764 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 764 " -0.032 5.00e-02 4.00e+02 ... (remaining 2139 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2632 2.77 - 3.30: 12633 3.30 - 3.84: 20695 3.84 - 4.37: 22471 4.37 - 4.90: 38730 Nonbonded interactions: 97161 Sorted by model distance: nonbonded pdb=" OD1 ASP A 250 " pdb=" N CYS A 251 " model vdw 2.241 3.120 nonbonded pdb=" OD1 ASP B 250 " pdb=" N CYS B 251 " model vdw 2.242 3.120 nonbonded pdb=" OE2 GLU A 670 " pdb="CA CA A1001 " model vdw 2.247 3.250 nonbonded pdb=" OE2 GLU B 670 " pdb="CA CA B1001 " model vdw 2.247 3.250 nonbonded pdb=" O VAL A 860 " pdb=" OG1 THR A 864 " model vdw 2.250 3.040 ... (remaining 97156 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.110 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.670 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 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 : 0.003 0.080 12638 Z= 0.136 Angle : 0.633 12.288 17152 Z= 0.318 Chirality : 0.041 0.228 1874 Planarity : 0.005 0.086 2142 Dihedral : 16.092 87.221 4598 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 21.92 % Favored : 78.08 % 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: 1.18 (0.23), residues: 1484 helix: 1.77 (0.18), residues: 868 sheet: 0.07 (0.65), residues: 68 loop : -0.73 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 277 TYR 0.022 0.001 TYR B 138 PHE 0.030 0.001 PHE B 852 TRP 0.034 0.001 TRP B 705 HIS 0.008 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (12628) covalent geometry : angle 0.63231 / 0.32 (17132) SS BOND : bond 0.00161 / 0.07 ( 10) SS BOND : angle 0.95588 / 0.61 ( 20) hydrogen bonds : bond 0.15076 / 9.82 ( 720) hydrogen bonds : angle 6.14432 / 4.41 ( 2106) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.492 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.0929 time to fit residues: 29.4781 Evaluate side-chains 189 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 HIS A 506 GLN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 HIS B 506 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.176660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.123515 restraints weight = 23949.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.127663 restraints weight = 10802.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.130133 restraints weight = 7234.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.131385 restraints weight = 5966.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.131774 restraints weight = 5466.401| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 12638 Z= 0.320 Angle : 0.734 10.918 17152 Z= 0.387 Chirality : 0.046 0.163 1874 Planarity : 0.005 0.049 2142 Dihedral : 4.551 17.597 1658 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 5.41 % Allowed : 17.79 % Favored : 76.80 % 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: 0.61 (0.22), residues: 1484 helix: 1.29 (0.17), residues: 872 sheet: -0.37 (0.60), residues: 68 loop : -0.91 (0.29), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 712 TYR 0.022 0.002 TYR B 138 PHE 0.023 0.002 PHE A 560 TRP 0.026 0.002 TRP B 705 HIS 0.005 0.001 HIS A 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00744 / 0.32 (12628) covalent geometry : angle 0.73222 / 0.39 (17132) SS BOND : bond 0.00523 / 0.24 ( 10) SS BOND : angle 1.60587 / 1.02 ( 20) hydrogen bonds : bond 0.04849 / 3.22 ( 720) hydrogen bonds : angle 5.00870 / 3.59 ( 2106) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 193 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7534 (mm-30) REVERT: A 125 PHE cc_start: 0.8443 (m-80) cc_final: 0.8236 (m-80) REVERT: A 196 TYR cc_start: 0.7381 (OUTLIER) cc_final: 0.5990 (t80) REVERT: A 624 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7221 (mt-10) REVERT: A 705 TRP cc_start: 0.8970 (t-100) cc_final: 0.8518 (t-100) REVERT: B 78 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7508 (mm-30) REVERT: B 125 PHE cc_start: 0.8469 (m-80) cc_final: 0.8266 (m-80) REVERT: B 196 TYR cc_start: 0.7421 (OUTLIER) cc_final: 0.6019 (t80) REVERT: B 624 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7222 (mt-10) REVERT: B 705 TRP cc_start: 0.8968 (t-100) cc_final: 0.8516 (t-100) outliers start: 72 outliers final: 33 residues processed: 242 average time/residue: 0.0852 time to fit residues: 32.5874 Evaluate side-chains 221 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 624 GLU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 839 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 121 optimal weight: 0.9990 chunk 75 optimal weight: 30.0000 chunk 38 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 4 optimal weight: 20.0000 chunk 125 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.180697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.129485 restraints weight = 23738.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.133826 restraints weight = 10408.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.136382 restraints weight = 6821.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.137781 restraints weight = 5547.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.138201 restraints weight = 5039.162| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12638 Z= 0.131 Angle : 0.602 14.260 17152 Z= 0.308 Chirality : 0.042 0.160 1874 Planarity : 0.005 0.054 2142 Dihedral : 4.244 17.165 1658 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.68 % Allowed : 19.14 % Favored : 77.18 % 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: 1.00 (0.22), residues: 1484 helix: 1.65 (0.17), residues: 872 sheet: -0.28 (0.62), residues: 68 loop : -0.82 (0.29), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 712 TYR 0.019 0.001 TYR B 138 PHE 0.017 0.001 PHE A 321 TRP 0.014 0.001 TRP A 397 HIS 0.002 0.001 HIS B 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (12628) covalent geometry : angle 0.60063 / 0.31 (17132) SS BOND : bond 0.00322 / 0.15 ( 10) SS BOND : angle 1.41333 / 0.87 ( 20) hydrogen bonds : bond 0.04006 / 2.67 ( 720) hydrogen bonds : angle 4.50743 / 3.22 ( 2106) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 211 time to evaluate : 0.479 Fit side-chains REVERT: A 78 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7443 (mm-30) REVERT: A 183 PHE cc_start: 0.6709 (OUTLIER) cc_final: 0.6291 (m-80) REVERT: A 196 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.6027 (t80) REVERT: A 405 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7859 (mm-30) REVERT: A 477 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.7284 (t80) REVERT: A 705 TRP cc_start: 0.8931 (t-100) cc_final: 0.8529 (t-100) REVERT: B 78 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7428 (mm-30) REVERT: B 127 LYS cc_start: 0.8424 (mttt) cc_final: 0.8178 (mttt) REVERT: B 183 PHE cc_start: 0.6662 (OUTLIER) cc_final: 0.6154 (m-80) REVERT: B 196 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.6083 (t80) REVERT: B 405 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7858 (mm-30) REVERT: B 477 TYR cc_start: 0.7723 (OUTLIER) cc_final: 0.7269 (t80) REVERT: B 613 MET cc_start: 0.9016 (mmm) cc_final: 0.8176 (mtt) REVERT: B 705 TRP cc_start: 0.8924 (t-100) cc_final: 0.8522 (t-100) outliers start: 49 outliers final: 26 residues processed: 246 average time/residue: 0.0815 time to fit residues: 32.0965 Evaluate side-chains 230 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 620 ASN Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 864 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 89 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 106 optimal weight: 10.0000 chunk 33 optimal weight: 0.0980 chunk 72 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 75 optimal weight: 30.0000 chunk 130 optimal weight: 6.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.179378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.127268 restraints weight = 23803.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.131587 restraints weight = 10546.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.134150 restraints weight = 6971.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.135465 restraints weight = 5695.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.135974 restraints weight = 5183.505| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12638 Z= 0.165 Angle : 0.607 14.323 17152 Z= 0.313 Chirality : 0.042 0.159 1874 Planarity : 0.005 0.056 2142 Dihedral : 4.227 16.740 1658 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.68 % Allowed : 20.72 % Favored : 75.60 % 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: 0.91 (0.22), residues: 1484 helix: 1.64 (0.17), residues: 872 sheet: -1.11 (0.53), residues: 88 loop : -0.83 (0.30), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 712 TYR 0.020 0.001 TYR B 138 PHE 0.023 0.002 PHE A 518 TRP 0.014 0.001 TRP A 397 HIS 0.002 0.001 HIS B 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (12628) covalent geometry : angle 0.60518 / 0.31 (17132) SS BOND : bond 0.00291 / 0.15 ( 10) SS BOND : angle 1.36460 / 0.84 ( 20) hydrogen bonds : bond 0.03952 / 2.63 ( 720) hydrogen bonds : angle 4.45845 / 3.19 ( 2106) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 203 time to evaluate : 0.375 Fit side-chains REVERT: A 78 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7481 (mm-30) REVERT: A 127 LYS cc_start: 0.8414 (mttt) cc_final: 0.7944 (mppt) REVERT: A 183 PHE cc_start: 0.6585 (OUTLIER) cc_final: 0.6094 (m-80) REVERT: A 196 TYR cc_start: 0.7409 (OUTLIER) cc_final: 0.5996 (t80) REVERT: A 405 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7914 (mm-30) REVERT: A 477 TYR cc_start: 0.7728 (OUTLIER) cc_final: 0.7270 (t80) REVERT: A 705 TRP cc_start: 0.8931 (t-100) cc_final: 0.8335 (t-100) REVERT: B 78 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7478 (mm-30) REVERT: B 127 LYS cc_start: 0.8514 (mttt) cc_final: 0.8227 (mptt) REVERT: B 183 PHE cc_start: 0.6499 (OUTLIER) cc_final: 0.6000 (m-80) REVERT: B 196 TYR cc_start: 0.7450 (OUTLIER) cc_final: 0.6056 (t80) REVERT: B 405 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7913 (mm-30) REVERT: B 477 TYR cc_start: 0.7696 (OUTLIER) cc_final: 0.7243 (t80) REVERT: B 705 TRP cc_start: 0.8932 (t-100) cc_final: 0.8337 (t-100) outliers start: 49 outliers final: 29 residues processed: 239 average time/residue: 0.0812 time to fit residues: 31.1053 Evaluate side-chains 226 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 621 ASN Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 864 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 0.5980 chunk 86 optimal weight: 8.9990 chunk 89 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.178149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.125794 restraints weight = 24035.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.130116 restraints weight = 10648.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.132639 restraints weight = 7051.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.133979 restraints weight = 5794.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.134419 restraints weight = 5281.341| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12638 Z= 0.199 Angle : 0.626 12.988 17152 Z= 0.325 Chirality : 0.043 0.184 1874 Planarity : 0.005 0.056 2142 Dihedral : 4.286 17.020 1658 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.28 % Allowed : 21.55 % Favored : 74.17 % 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: 0.81 (0.22), residues: 1484 helix: 1.55 (0.17), residues: 874 sheet: -1.28 (0.51), residues: 88 loop : -0.84 (0.30), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 639 TYR 0.020 0.001 TYR B 138 PHE 0.023 0.002 PHE B 321 TRP 0.015 0.001 TRP A 397 HIS 0.005 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (12628) covalent geometry : angle 0.62463 / 0.32 (17132) SS BOND : bond 0.00321 / 0.16 ( 10) SS BOND : angle 1.35284 / 0.83 ( 20) hydrogen bonds : bond 0.04072 / 2.70 ( 720) hydrogen bonds : angle 4.54178 / 3.26 ( 2106) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 203 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7527 (mm-30) REVERT: A 127 LYS cc_start: 0.8499 (mttt) cc_final: 0.8255 (mttt) REVERT: A 183 PHE cc_start: 0.6555 (OUTLIER) cc_final: 0.6004 (m-80) REVERT: A 196 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.5984 (t80) REVERT: A 405 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7926 (mm-30) REVERT: B 78 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7532 (mm-30) REVERT: B 127 LYS cc_start: 0.8455 (mttt) cc_final: 0.8071 (mttt) REVERT: B 183 PHE cc_start: 0.6476 (OUTLIER) cc_final: 0.5922 (m-80) REVERT: B 196 TYR cc_start: 0.7457 (OUTLIER) cc_final: 0.6042 (t80) REVERT: B 405 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7923 (mm-30) REVERT: B 456 CYS cc_start: 0.8253 (m) cc_final: 0.7972 (p) outliers start: 57 outliers final: 39 residues processed: 247 average time/residue: 0.0927 time to fit residues: 35.6621 Evaluate side-chains 236 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 193 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 620 ASN Chi-restraints excluded: chain B residue 621 ASN Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 864 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 57 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 2 optimal weight: 30.0000 chunk 51 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 121 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.182250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.130817 restraints weight = 23877.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.135265 restraints weight = 10433.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.137921 restraints weight = 6816.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.139045 restraints weight = 5517.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.139843 restraints weight = 5043.348| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12638 Z= 0.117 Angle : 0.595 16.812 17152 Z= 0.302 Chirality : 0.042 0.203 1874 Planarity : 0.005 0.058 2142 Dihedral : 4.125 17.720 1658 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.70 % Allowed : 22.90 % Favored : 74.40 % 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: 1.05 (0.22), residues: 1484 helix: 1.83 (0.17), residues: 872 sheet: -1.32 (0.53), residues: 86 loop : -0.88 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 542 TYR 0.020 0.001 TYR A 770 PHE 0.019 0.001 PHE B 321 TRP 0.014 0.001 TRP A 397 HIS 0.004 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (12628) covalent geometry : angle 0.59396 / 0.30 (17132) SS BOND : bond 0.00286 / 0.15 ( 10) SS BOND : angle 1.29995 / 0.79 ( 20) hydrogen bonds : bond 0.03583 / 2.38 ( 720) hydrogen bonds : angle 4.32757 / 3.11 ( 2106) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 214 time to evaluate : 0.530 Fit side-chains REVERT: A 127 LYS cc_start: 0.8443 (mttt) cc_final: 0.8162 (mttt) REVERT: A 183 PHE cc_start: 0.6687 (OUTLIER) cc_final: 0.6168 (m-80) REVERT: A 196 TYR cc_start: 0.7440 (OUTLIER) cc_final: 0.6075 (t80) REVERT: A 309 MET cc_start: 0.8019 (tpp) cc_final: 0.7805 (tpt) REVERT: A 405 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7986 (mm-30) REVERT: A 477 TYR cc_start: 0.7768 (OUTLIER) cc_final: 0.7344 (t80) REVERT: A 613 MET cc_start: 0.8980 (mmm) cc_final: 0.8236 (mtt) REVERT: A 655 HIS cc_start: 0.8518 (m90) cc_final: 0.8134 (m90) REVERT: A 705 TRP cc_start: 0.8914 (t-100) cc_final: 0.8417 (t-100) REVERT: B 115 THR cc_start: 0.7252 (OUTLIER) cc_final: 0.6481 (p) REVERT: B 127 LYS cc_start: 0.8391 (mttt) cc_final: 0.8103 (mptt) REVERT: B 183 PHE cc_start: 0.6637 (OUTLIER) cc_final: 0.5979 (m-80) REVERT: B 196 TYR cc_start: 0.7475 (OUTLIER) cc_final: 0.6126 (t80) REVERT: B 309 MET cc_start: 0.8230 (tpp) cc_final: 0.7758 (tpp) REVERT: B 405 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7946 (mm-30) REVERT: B 456 CYS cc_start: 0.8279 (m) cc_final: 0.7994 (p) REVERT: B 477 TYR cc_start: 0.7727 (OUTLIER) cc_final: 0.7311 (t80) REVERT: B 517 SER cc_start: 0.9149 (m) cc_final: 0.8948 (p) REVERT: B 613 MET cc_start: 0.8981 (mmm) cc_final: 0.8237 (mtt) REVERT: B 705 TRP cc_start: 0.8914 (t-100) cc_final: 0.8415 (t-100) outliers start: 36 outliers final: 21 residues processed: 240 average time/residue: 0.0897 time to fit residues: 34.4057 Evaluate side-chains 232 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 621 ASN Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 864 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 26 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.182220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.130406 restraints weight = 23850.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.134863 restraints weight = 10457.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.137471 restraints weight = 6847.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.138956 restraints weight = 5566.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.139382 restraints weight = 5043.053| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12638 Z= 0.125 Angle : 0.606 15.458 17152 Z= 0.307 Chirality : 0.042 0.194 1874 Planarity : 0.005 0.059 2142 Dihedral : 4.080 16.641 1658 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.53 % Allowed : 22.97 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.22), residues: 1484 helix: 1.87 (0.17), residues: 872 sheet: -1.17 (0.52), residues: 88 loop : -0.87 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 542 TYR 0.021 0.001 TYR B 591 PHE 0.026 0.001 PHE B 518 TRP 0.013 0.001 TRP B 397 HIS 0.003 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (12628) covalent geometry : angle 0.60492 / 0.31 (17132) SS BOND : bond 0.00288 / 0.15 ( 10) SS BOND : angle 1.28298 / 0.80 ( 20) hydrogen bonds : bond 0.03647 / 2.43 ( 720) hydrogen bonds : angle 4.31718 / 3.11 ( 2106) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 202 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: A 127 LYS cc_start: 0.8405 (mttt) cc_final: 0.8109 (mttt) REVERT: A 183 PHE cc_start: 0.6721 (OUTLIER) cc_final: 0.6073 (m-80) REVERT: A 196 TYR cc_start: 0.7431 (OUTLIER) cc_final: 0.6086 (t80) REVERT: A 309 MET cc_start: 0.8030 (tpp) cc_final: 0.7820 (tpt) REVERT: A 405 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7971 (mm-30) REVERT: A 477 TYR cc_start: 0.7726 (OUTLIER) cc_final: 0.7288 (t80) REVERT: A 613 MET cc_start: 0.8983 (mmm) cc_final: 0.8163 (mtt) REVERT: A 655 HIS cc_start: 0.8588 (m90) cc_final: 0.8060 (m-70) REVERT: A 710 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8053 (mm-40) REVERT: B 127 LYS cc_start: 0.8388 (mttt) cc_final: 0.8077 (mttt) REVERT: B 183 PHE cc_start: 0.6657 (OUTLIER) cc_final: 0.6031 (m-80) REVERT: B 196 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.6127 (t80) REVERT: B 309 MET cc_start: 0.8238 (tpp) cc_final: 0.7734 (tpp) REVERT: B 405 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7942 (mm-30) REVERT: B 456 CYS cc_start: 0.8320 (m) cc_final: 0.8025 (p) REVERT: B 477 TYR cc_start: 0.7707 (OUTLIER) cc_final: 0.7277 (t80) REVERT: B 613 MET cc_start: 0.8984 (mmm) cc_final: 0.8176 (mtt) REVERT: B 655 HIS cc_start: 0.8478 (m90) cc_final: 0.8101 (m90) REVERT: B 705 TRP cc_start: 0.8921 (t-100) cc_final: 0.8323 (t-100) outliers start: 47 outliers final: 33 residues processed: 234 average time/residue: 0.0884 time to fit residues: 33.2333 Evaluate side-chains 231 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 637 TYR Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 710 GLN Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 621 ASN Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 864 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 34 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 147 optimal weight: 0.6980 chunk 47 optimal weight: 0.0020 chunk 106 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.184017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.132966 restraints weight = 23912.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.137477 restraints weight = 10485.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.140184 restraints weight = 6807.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.141680 restraints weight = 5485.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.141993 restraints weight = 4936.358| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12638 Z= 0.113 Angle : 0.610 18.771 17152 Z= 0.305 Chirality : 0.041 0.216 1874 Planarity : 0.005 0.060 2142 Dihedral : 3.995 16.865 1658 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.78 % Allowed : 23.87 % Favored : 73.35 % 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: 1.22 (0.23), residues: 1484 helix: 1.97 (0.17), residues: 870 sheet: -1.16 (0.54), residues: 86 loop : -0.82 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 639 TYR 0.024 0.001 TYR B 770 PHE 0.028 0.001 PHE B 385 TRP 0.014 0.001 TRP B 397 HIS 0.003 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (12628) covalent geometry : angle 0.60842 / 0.30 (17132) SS BOND : bond 0.00269 / 0.13 ( 10) SS BOND : angle 1.27451 / 0.79 ( 20) hydrogen bonds : bond 0.03500 / 2.33 ( 720) hydrogen bonds : angle 4.26237 / 3.06 ( 2106) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 0.463 Fit side-chains REVERT: A 78 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7517 (mm-30) REVERT: A 127 LYS cc_start: 0.8411 (mttt) cc_final: 0.8131 (mttt) REVERT: A 183 PHE cc_start: 0.6956 (OUTLIER) cc_final: 0.6202 (m-80) REVERT: A 309 MET cc_start: 0.7956 (tpp) cc_final: 0.7747 (tpt) REVERT: A 405 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7959 (mm-30) REVERT: A 456 CYS cc_start: 0.8295 (m) cc_final: 0.7948 (p) REVERT: A 477 TYR cc_start: 0.7689 (OUTLIER) cc_final: 0.7204 (t80) REVERT: A 613 MET cc_start: 0.8940 (mmm) cc_final: 0.8181 (mtt) REVERT: A 655 HIS cc_start: 0.8637 (m90) cc_final: 0.7987 (m-70) REVERT: A 705 TRP cc_start: 0.8885 (t-100) cc_final: 0.8336 (t-100) REVERT: A 710 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7954 (mm110) REVERT: B 127 LYS cc_start: 0.8328 (mttt) cc_final: 0.8027 (mttt) REVERT: B 183 PHE cc_start: 0.6782 (OUTLIER) cc_final: 0.6009 (m-80) REVERT: B 309 MET cc_start: 0.8130 (tpp) cc_final: 0.7671 (tpp) REVERT: B 405 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7945 (mm-30) REVERT: B 456 CYS cc_start: 0.8338 (m) cc_final: 0.8028 (p) REVERT: B 477 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.7186 (t80) REVERT: B 613 MET cc_start: 0.8928 (mmm) cc_final: 0.8184 (mtt) REVERT: B 655 HIS cc_start: 0.8623 (m90) cc_final: 0.8081 (m-70) outliers start: 37 outliers final: 28 residues processed: 242 average time/residue: 0.0749 time to fit residues: 29.2158 Evaluate side-chains 235 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 637 TYR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 710 GLN Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 621 ASN Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 864 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 62 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 75 optimal weight: 30.0000 chunk 94 optimal weight: 0.5980 chunk 118 optimal weight: 9.9990 chunk 82 optimal weight: 20.0000 chunk 69 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.183293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.132143 restraints weight = 23752.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.136644 restraints weight = 10500.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.139280 restraints weight = 6849.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.140764 restraints weight = 5534.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.141510 restraints weight = 4983.387| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12638 Z= 0.123 Angle : 0.624 17.561 17152 Z= 0.312 Chirality : 0.042 0.204 1874 Planarity : 0.004 0.060 2142 Dihedral : 3.980 16.542 1658 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.63 % Allowed : 24.02 % Favored : 73.35 % 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: 1.23 (0.22), residues: 1484 helix: 1.97 (0.17), residues: 868 sheet: -1.16 (0.54), residues: 86 loop : -0.80 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 639 TYR 0.020 0.001 TYR B 138 PHE 0.026 0.001 PHE A 518 TRP 0.012 0.001 TRP A 397 HIS 0.003 0.001 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (12628) covalent geometry : angle 0.62272 / 0.31 (17132) SS BOND : bond 0.00235 / 0.12 ( 10) SS BOND : angle 1.24806 / 0.77 ( 20) hydrogen bonds : bond 0.03526 / 2.34 ( 720) hydrogen bonds : angle 4.25015 / 3.05 ( 2106) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 210 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7503 (mm-30) REVERT: A 127 LYS cc_start: 0.8403 (mttt) cc_final: 0.8144 (mttt) REVERT: A 183 PHE cc_start: 0.6945 (OUTLIER) cc_final: 0.6190 (m-80) REVERT: A 309 MET cc_start: 0.8000 (tpp) cc_final: 0.7778 (tpt) REVERT: A 405 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7976 (mm-30) REVERT: A 456 CYS cc_start: 0.8307 (m) cc_final: 0.7953 (p) REVERT: A 477 TYR cc_start: 0.7657 (OUTLIER) cc_final: 0.7172 (t80) REVERT: A 613 MET cc_start: 0.8931 (mmm) cc_final: 0.8159 (mtt) REVERT: A 655 HIS cc_start: 0.8612 (m90) cc_final: 0.7960 (m-70) REVERT: A 710 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7860 (mm110) REVERT: B 78 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7510 (mm-30) REVERT: B 127 LYS cc_start: 0.8325 (mttt) cc_final: 0.8057 (mttt) REVERT: B 183 PHE cc_start: 0.6797 (OUTLIER) cc_final: 0.6040 (m-80) REVERT: B 309 MET cc_start: 0.8176 (tpp) cc_final: 0.7676 (tpp) REVERT: B 405 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7969 (mm-30) REVERT: B 456 CYS cc_start: 0.8352 (m) cc_final: 0.8037 (p) REVERT: B 477 TYR cc_start: 0.7614 (OUTLIER) cc_final: 0.7146 (t80) REVERT: B 613 MET cc_start: 0.8926 (mmm) cc_final: 0.8187 (mtt) REVERT: B 655 HIS cc_start: 0.8591 (m90) cc_final: 0.7951 (m-70) outliers start: 35 outliers final: 28 residues processed: 236 average time/residue: 0.0753 time to fit residues: 28.9904 Evaluate side-chains 229 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 637 TYR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 710 GLN Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 621 ASN Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 864 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 135 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 2 optimal weight: 30.0000 chunk 104 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.179579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.127737 restraints weight = 23921.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.132061 restraints weight = 10601.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.134626 restraints weight = 6963.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.136011 restraints weight = 5655.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.136338 restraints weight = 5128.753| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12638 Z= 0.194 Angle : 0.674 16.648 17152 Z= 0.341 Chirality : 0.043 0.195 1874 Planarity : 0.005 0.059 2142 Dihedral : 4.179 16.716 1658 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.93 % Allowed : 23.80 % Favored : 73.27 % 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: 1.03 (0.22), residues: 1484 helix: 1.76 (0.17), residues: 872 sheet: -1.13 (0.52), residues: 88 loop : -0.82 (0.30), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 712 TYR 0.022 0.001 TYR B 138 PHE 0.024 0.002 PHE A 385 TRP 0.010 0.001 TRP A 302 HIS 0.003 0.001 HIS A 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 (12628) covalent geometry : angle 0.67299 / 0.34 (17132) SS BOND : bond 0.00299 / 0.15 ( 10) SS BOND : angle 1.29363 / 0.80 ( 20) hydrogen bonds : bond 0.03935 / 2.62 ( 720) hydrogen bonds : angle 4.37393 / 3.13 ( 2106) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 PHE cc_start: 0.6685 (OUTLIER) cc_final: 0.5841 (m-80) REVERT: A 309 MET cc_start: 0.8291 (tpp) cc_final: 0.8066 (tpt) REVERT: A 405 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7939 (mm-30) REVERT: A 477 TYR cc_start: 0.7685 (OUTLIER) cc_final: 0.7188 (t80) REVERT: A 655 HIS cc_start: 0.8587 (m90) cc_final: 0.8122 (m90) REVERT: A 710 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8268 (mm110) REVERT: B 127 LYS cc_start: 0.8361 (mttt) cc_final: 0.7963 (mttt) REVERT: B 183 PHE cc_start: 0.6711 (OUTLIER) cc_final: 0.5884 (m-80) REVERT: B 405 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7969 (mm-30) REVERT: B 477 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.7170 (t80) REVERT: B 613 MET cc_start: 0.9035 (mmm) cc_final: 0.8306 (mtt) outliers start: 39 outliers final: 30 residues processed: 232 average time/residue: 0.0749 time to fit residues: 28.0193 Evaluate side-chains 233 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 198 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 637 TYR Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 710 GLN Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 620 ASN Chi-restraints excluded: chain B residue 621 ASN Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 864 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 138 optimal weight: 0.7980 chunk 149 optimal weight: 0.0670 chunk 125 optimal weight: 0.9990 chunk 91 optimal weight: 0.4980 chunk 18 optimal weight: 8.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.184123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.132790 restraints weight = 23657.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.137347 restraints weight = 10599.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.140054 restraints weight = 6915.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.141525 restraints weight = 5581.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.141868 restraints weight = 5029.054| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12638 Z= 0.120 Angle : 0.657 17.362 17152 Z= 0.323 Chirality : 0.042 0.207 1874 Planarity : 0.004 0.059 2142 Dihedral : 4.049 17.036 1658 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.40 % Allowed : 25.68 % Favored : 71.92 % 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: 1.14 (0.22), residues: 1484 helix: 1.90 (0.17), residues: 868 sheet: -1.16 (0.55), residues: 86 loop : -0.84 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 712 TYR 0.021 0.001 TYR B 138 PHE 0.020 0.001 PHE A 385 TRP 0.015 0.001 TRP B 397 HIS 0.004 0.001 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (12628) covalent geometry : angle 0.65590 / 0.32 (17132) SS BOND : bond 0.00223 / 0.11 ( 10) SS BOND : angle 1.23828 / 0.77 ( 20) hydrogen bonds : bond 0.03508 / 2.33 ( 720) hydrogen bonds : angle 4.27273 / 3.06 ( 2106) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2434.37 seconds wall clock time: 42 minutes 43.46 seconds (2563.46 seconds total)