Starting phenix.real_space_refine on Thu Jun 4 11:11:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o1n_70013/06_2026/9o1n_70013.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o1n_70013/06_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_70013/06_2026/9o1n_70013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o1n_70013/06_2026/9o1n_70013.map" model { file = "/net/cci-nas-00/data/ceres_data/9o1n_70013/06_2026/9o1n_70013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o1n_70013/06_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-6079/lib/python3.9/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, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B Time building chain proxies: 5.70, per 1000 atoms: 0.46 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: 0.91 Conformation dependent library (CDL) restraints added in 529.1 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: 0.32 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: 1.70 Time building geometry restraints manager: 1.30 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 2.510 nonbonded pdb=" OE2 GLU B 670 " pdb="CA CA B1001 " model vdw 2.247 2.510 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: 0.01 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.680 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 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 : 0.530 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.0824 time to fit residues: 26.1806 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 : 0.366 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4436 r_free = 0.4436 target = 0.177197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.124046 restraints weight = 23929.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.128264 restraints weight = 10823.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.130678 restraints weight = 7261.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.131856 restraints weight = 6008.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.132112 restraints weight = 5511.006| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1771 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 : 0.740 10.601 17152 Z= 0.392 Chirality : 0.047 0.164 1874 Planarity : 0.006 0.049 2142 Dihedral : 4.611 18.068 1658 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 5.48 % Allowed : 17.57 % Favored : 76.95 % 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: 0.57 (0.22), residues: 1484 helix: 1.24 (0.17), residues: 864 sheet: -0.40 (0.60), residues: 68 loop : -0.84 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 712 TYR 0.024 0.002 TYR B 138 PHE 0.023 0.002 PHE A 852 TRP 0.025 0.002 TRP B 705 HIS 0.006 0.001 HIS B 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00742 / 0.32 (12628) covalent geometry : angle 0.73800 / 0.39 (17132) SS BOND : bond 0.00527 / 0.25 ( 10) SS BOND : angle 1.62769 / 1.03 ( 20) hydrogen bonds : bond 0.04851 / 3.22 ( 720) hydrogen bonds : angle 4.99912 / 3.58 ( 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 263 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 190 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7578 (mm-30) REVERT: A 125 PHE cc_start: 0.8456 (m-80) cc_final: 0.8233 (m-80) REVERT: A 196 TYR cc_start: 0.7366 (OUTLIER) cc_final: 0.5971 (t80) REVERT: A 667 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7660 (mm-30) REVERT: A 705 TRP cc_start: 0.8988 (t-100) cc_final: 0.8467 (t-100) REVERT: B 78 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7531 (mm-30) REVERT: B 125 PHE cc_start: 0.8478 (m-80) cc_final: 0.8257 (m-80) REVERT: B 196 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.5990 (t80) REVERT: B 667 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7663 (mm-30) REVERT: B 705 TRP cc_start: 0.8989 (t-100) cc_final: 0.8468 (t-100) outliers start: 73 outliers final: 37 residues processed: 240 average time/residue: 0.0824 time to fit residues: 31.1722 Evaluate side-chains 219 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 326 LEU 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 826 ILE 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: 2.9990 chunk 75 optimal weight: 30.0000 chunk 38 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 4 optimal weight: 20.0000 chunk 125 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN B 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.180930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.129641 restraints weight = 23749.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.133964 restraints weight = 10494.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.136576 restraints weight = 6908.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.137970 restraints weight = 5613.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.138499 restraints weight = 5088.329| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12638 Z= 0.128 Angle : 0.599 14.237 17152 Z= 0.306 Chirality : 0.042 0.160 1874 Planarity : 0.005 0.055 2142 Dihedral : 4.257 17.296 1658 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.30 % Allowed : 19.74 % Favored : 76.95 % 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: 0.96 (0.22), residues: 1484 helix: 1.61 (0.17), residues: 872 sheet: -0.30 (0.62), residues: 68 loop : -0.83 (0.29), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 712 TYR 0.020 0.001 TYR B 138 PHE 0.017 0.001 PHE A 321 TRP 0.015 0.001 TRP B 705 HIS 0.002 0.001 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (12628) covalent geometry : angle 0.59711 / 0.31 (17132) SS BOND : bond 0.00320 / 0.16 ( 10) SS BOND : angle 1.38149 / 0.84 ( 20) hydrogen bonds : bond 0.03992 / 2.66 ( 720) hydrogen bonds : angle 4.49104 / 3.20 ( 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 257 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 213 time to evaluate : 0.437 Fit side-chains REVERT: A 78 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7444 (mm-30) REVERT: A 127 LYS cc_start: 0.8436 (mttt) cc_final: 0.8184 (mttt) REVERT: A 183 PHE cc_start: 0.6700 (OUTLIER) cc_final: 0.6189 (m-80) REVERT: A 196 TYR cc_start: 0.7402 (OUTLIER) cc_final: 0.6008 (t80) REVERT: A 405 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7866 (mm-30) REVERT: A 477 TYR cc_start: 0.7731 (OUTLIER) cc_final: 0.7292 (t80) REVERT: A 624 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6830 (mt-10) REVERT: A 705 TRP cc_start: 0.8951 (t-100) cc_final: 0.8541 (t-100) REVERT: B 78 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7448 (mm-30) REVERT: B 127 LYS cc_start: 0.8436 (mttt) cc_final: 0.8184 (mttt) REVERT: B 183 PHE cc_start: 0.6654 (OUTLIER) cc_final: 0.6148 (m-80) REVERT: B 196 TYR cc_start: 0.7482 (OUTLIER) cc_final: 0.6086 (t80) REVERT: B 405 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7862 (mm-30) REVERT: B 477 TYR cc_start: 0.7734 (OUTLIER) cc_final: 0.7268 (t80) REVERT: B 624 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6837 (mt-10) REVERT: B 705 TRP cc_start: 0.8951 (t-100) cc_final: 0.8542 (t-100) outliers start: 44 outliers final: 25 residues processed: 240 average time/residue: 0.0837 time to fit residues: 32.1367 Evaluate side-chains 237 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 624 GLU Chi-restraints excluded: chain A residue 625 VAL 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 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 624 GLU Chi-restraints excluded: chain B residue 625 VAL 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: 6.9990 chunk 103 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 106 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 75 optimal weight: 30.0000 chunk 130 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.179054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.126782 restraints weight = 23917.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.131062 restraints weight = 10640.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.133619 restraints weight = 7068.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.134927 restraints weight = 5784.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.135342 restraints weight = 5276.783| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12638 Z= 0.174 Angle : 0.613 14.064 17152 Z= 0.316 Chirality : 0.042 0.165 1874 Planarity : 0.005 0.056 2142 Dihedral : 4.250 16.671 1658 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.35 % Allowed : 20.35 % Favored : 75.30 % 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: 0.86 (0.22), residues: 1484 helix: 1.59 (0.17), residues: 872 sheet: -1.10 (0.53), residues: 88 loop : -0.85 (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 B 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 0.00409 / 0.17 (12628) covalent geometry : angle 0.61112 / 0.32 (17132) SS BOND : bond 0.00301 / 0.15 ( 10) SS BOND : angle 1.35957 / 0.83 ( 20) hydrogen bonds : bond 0.03999 / 2.66 ( 720) hydrogen bonds : angle 4.46340 / 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 260 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 202 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7494 (mm-30) REVERT: A 127 LYS cc_start: 0.8482 (mttt) cc_final: 0.8209 (mptt) REVERT: A 183 PHE cc_start: 0.6514 (OUTLIER) cc_final: 0.6045 (m-80) REVERT: A 196 TYR cc_start: 0.7410 (OUTLIER) cc_final: 0.5996 (t80) REVERT: A 405 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7919 (mm-30) REVERT: A 705 TRP cc_start: 0.8955 (t-100) cc_final: 0.8320 (t-100) REVERT: B 78 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7472 (mm-30) REVERT: B 127 LYS cc_start: 0.8483 (mttt) cc_final: 0.8206 (mptt) REVERT: B 183 PHE cc_start: 0.6487 (OUTLIER) cc_final: 0.5998 (m-80) REVERT: B 196 TYR cc_start: 0.7458 (OUTLIER) cc_final: 0.6078 (t80) REVERT: B 405 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7934 (mm-30) REVERT: B 705 TRP cc_start: 0.8957 (t-100) cc_final: 0.8323 (t-100) outliers start: 58 outliers final: 31 residues processed: 247 average time/residue: 0.0780 time to fit residues: 30.9413 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 : 0.457 ------------------------------------------------------------------------------- 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 543 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 633 LEU 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 543 THR Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 624 GLU 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 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: 0.4980 chunk 86 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.179018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.126785 restraints weight = 23901.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.131074 restraints weight = 10607.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.133547 restraints weight = 7048.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.134935 restraints weight = 5785.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.135365 restraints weight = 5267.875| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12638 Z= 0.170 Angle : 0.603 12.858 17152 Z= 0.313 Chirality : 0.042 0.187 1874 Planarity : 0.005 0.057 2142 Dihedral : 4.237 17.042 1658 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.05 % Allowed : 21.70 % Favored : 74.25 % 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: 0.88 (0.22), residues: 1484 helix: 1.63 (0.17), residues: 872 sheet: -1.23 (0.52), residues: 88 loop : -0.85 (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 0.021 0.001 PHE B 321 TRP 0.014 0.001 TRP A 397 HIS 0.002 0.001 HIS A 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (12628) covalent geometry : angle 0.60138 / 0.31 (17132) SS BOND : bond 0.00302 / 0.15 ( 10) SS BOND : angle 1.35926 / 0.83 ( 20) hydrogen bonds : bond 0.03908 / 2.60 ( 720) hydrogen bonds : angle 4.40415 / 3.15 ( 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 261 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 207 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7546 (mm-30) REVERT: A 127 LYS cc_start: 0.8430 (mttt) cc_final: 0.8065 (mttt) REVERT: A 183 PHE cc_start: 0.6605 (OUTLIER) cc_final: 0.6065 (m-80) REVERT: A 196 TYR cc_start: 0.7396 (OUTLIER) cc_final: 0.5991 (t80) REVERT: A 405 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7936 (mm-30) REVERT: A 477 TYR cc_start: 0.7757 (OUTLIER) cc_final: 0.7274 (t80) REVERT: B 78 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7512 (mm-30) REVERT: B 127 LYS cc_start: 0.8429 (mttt) cc_final: 0.8063 (mttt) REVERT: B 183 PHE cc_start: 0.6465 (OUTLIER) cc_final: 0.5921 (m-80) REVERT: B 196 TYR cc_start: 0.7458 (OUTLIER) cc_final: 0.6064 (t80) REVERT: B 405 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7933 (mm-30) REVERT: B 456 CYS cc_start: 0.8259 (m) cc_final: 0.7974 (p) REVERT: B 477 TYR cc_start: 0.7718 (OUTLIER) cc_final: 0.7218 (t80) outliers start: 54 outliers final: 38 residues processed: 247 average time/residue: 0.0862 time to fit residues: 33.6002 Evaluate side-chains 239 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 477 TYR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 633 LEU 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 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 624 GLU 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 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: 0.9990 chunk 105 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 74 optimal weight: 20.0000 chunk 121 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.182133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.130575 restraints weight = 23882.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.135014 restraints weight = 10553.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.137631 restraints weight = 6916.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.139157 restraints weight = 5617.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.139480 restraints weight = 5072.062| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12638 Z= 0.117 Angle : 0.608 16.341 17152 Z= 0.304 Chirality : 0.041 0.195 1874 Planarity : 0.005 0.058 2142 Dihedral : 4.110 16.605 1658 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.00 % Allowed : 23.05 % Favored : 73.95 % 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: 1.08 (0.23), residues: 1484 helix: 1.84 (0.17), residues: 872 sheet: -1.24 (0.52), residues: 88 loop : -0.85 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 542 TYR 0.019 0.001 TYR B 138 PHE 0.026 0.001 PHE A 518 TRP 0.014 0.001 TRP A 397 HIS 0.002 0.001 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (12628) covalent geometry : angle 0.60677 / 0.30 (17132) SS BOND : bond 0.00305 / 0.17 ( 10) SS BOND : angle 1.28919 / 0.79 ( 20) hydrogen bonds : bond 0.03622 / 2.41 ( 720) hydrogen bonds : angle 4.29223 / 3.07 ( 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 261 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 221 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7532 (mm-30) REVERT: A 127 LYS cc_start: 0.8408 (mttt) cc_final: 0.8068 (mttt) REVERT: A 183 PHE cc_start: 0.6720 (OUTLIER) cc_final: 0.6194 (m-80) REVERT: A 196 TYR cc_start: 0.7441 (OUTLIER) cc_final: 0.6089 (t80) REVERT: A 309 MET cc_start: 0.8214 (tpp) cc_final: 0.7714 (tpp) REVERT: A 405 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7967 (mm-30) REVERT: A 477 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.7365 (t80) REVERT: A 533 ILE cc_start: 0.8797 (tt) cc_final: 0.8588 (tp) REVERT: A 613 MET cc_start: 0.9005 (mmm) cc_final: 0.8221 (mtt) REVERT: A 624 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6691 (mt-10) REVERT: A 705 TRP cc_start: 0.8916 (t-100) cc_final: 0.8388 (t-100) REVERT: B 127 LYS cc_start: 0.8404 (mttt) cc_final: 0.8100 (mptt) REVERT: B 183 PHE cc_start: 0.6643 (OUTLIER) cc_final: 0.5989 (m-80) REVERT: B 196 TYR cc_start: 0.7487 (OUTLIER) cc_final: 0.6132 (t80) REVERT: B 309 MET cc_start: 0.8213 (tpp) cc_final: 0.7649 (tpp) REVERT: B 405 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7928 (mm-30) REVERT: B 456 CYS cc_start: 0.8274 (m) cc_final: 0.7971 (p) REVERT: B 477 TYR cc_start: 0.7745 (OUTLIER) cc_final: 0.7321 (t80) REVERT: B 613 MET cc_start: 0.9006 (mmm) cc_final: 0.8222 (mtt) REVERT: B 624 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6696 (mt-10) REVERT: B 705 TRP cc_start: 0.8921 (t-100) cc_final: 0.8398 (t-100) outliers start: 40 outliers final: 27 residues processed: 249 average time/residue: 0.0840 time to fit residues: 33.4991 Evaluate side-chains 239 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 204 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 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 624 GLU Chi-restraints excluded: chain A residue 693 LEU 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 624 GLU Chi-restraints excluded: chain B residue 693 LEU 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: 5.9990 chunk 22 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 59 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.181462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.130363 restraints weight = 23740.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.134671 restraints weight = 10567.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.137309 restraints weight = 6932.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.138285 restraints weight = 5612.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.139251 restraints weight = 5138.312| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1964 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= 0.129 Angle : 0.607 15.021 17152 Z= 0.309 Chirality : 0.042 0.203 1874 Planarity : 0.005 0.059 2142 Dihedral : 4.071 16.122 1658 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.15 % Allowed : 22.82 % Favored : 74.02 % 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: 1.07 (0.22), residues: 1484 helix: 1.85 (0.17), residues: 872 sheet: -1.30 (0.53), residues: 86 loop : -0.88 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 542 TYR 0.021 0.001 TYR B 138 PHE 0.026 0.001 PHE B 518 TRP 0.013 0.001 TRP A 397 HIS 0.003 0.001 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (12628) covalent geometry : angle 0.60605 / 0.31 (17132) SS BOND : bond 0.00293 / 0.15 ( 10) SS BOND : angle 1.26562 / 0.79 ( 20) hydrogen bonds : bond 0.03616 / 2.41 ( 720) hydrogen bonds : angle 4.29817 / 3.07 ( 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 242 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 200 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7542 (mm-30) REVERT: A 127 LYS cc_start: 0.8364 (mttt) cc_final: 0.8079 (mttt) REVERT: A 183 PHE cc_start: 0.6758 (OUTLIER) cc_final: 0.6112 (m-80) REVERT: A 309 MET cc_start: 0.8287 (tpp) cc_final: 0.7748 (tpp) REVERT: A 405 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7970 (mm-30) REVERT: A 477 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.7292 (t80) REVERT: A 624 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6657 (mt-10) REVERT: A 710 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8114 (mm-40) REVERT: B 127 LYS cc_start: 0.8367 (mttt) cc_final: 0.8074 (mttt) REVERT: B 183 PHE cc_start: 0.6665 (OUTLIER) cc_final: 0.6026 (m-80) REVERT: B 309 MET cc_start: 0.8298 (tpp) cc_final: 0.7778 (tpp) REVERT: B 405 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7965 (mm-30) REVERT: B 456 CYS cc_start: 0.8317 (m) cc_final: 0.8006 (p) REVERT: B 477 TYR cc_start: 0.7716 (OUTLIER) cc_final: 0.7272 (t80) REVERT: B 613 MET cc_start: 0.9011 (mmm) cc_final: 0.8187 (mtt) REVERT: B 624 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6659 (mt-10) REVERT: B 710 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8108 (mm-40) outliers start: 42 outliers final: 32 residues processed: 230 average time/residue: 0.0784 time to fit residues: 29.1162 Evaluate side-chains 233 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 193 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 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 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 624 GLU Chi-restraints excluded: chain A residue 625 VAL 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 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 620 ASN Chi-restraints excluded: chain B residue 621 ASN Chi-restraints excluded: chain B residue 624 GLU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 710 GLN 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: 3.9990 chunk 97 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 47 optimal weight: 0.0770 chunk 106 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 30.0000 overall best weight: 0.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN A 695 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.183842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.133213 restraints weight = 23920.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.137607 restraints weight = 10615.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.140340 restraints weight = 6917.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.141485 restraints weight = 5556.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.142486 restraints weight = 5062.330| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 12638 Z= 0.115 Angle : 0.613 18.348 17152 Z= 0.307 Chirality : 0.041 0.207 1874 Planarity : 0.004 0.060 2142 Dihedral : 3.996 16.030 1658 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.15 % Allowed : 23.42 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.22), residues: 1484 helix: 1.93 (0.17), residues: 872 sheet: -1.25 (0.53), residues: 86 loop : -0.89 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 636 TYR 0.024 0.001 TYR B 770 PHE 0.031 0.001 PHE B 385 TRP 0.013 0.001 TRP A 397 HIS 0.003 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (12628) covalent geometry : angle 0.61149 / 0.31 (17132) SS BOND : bond 0.00272 / 0.13 ( 10) SS BOND : angle 1.26275 / 0.79 ( 20) hydrogen bonds : bond 0.03513 / 2.34 ( 720) hydrogen bonds : angle 4.28009 / 3.07 ( 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 251 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 209 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7519 (mm-30) REVERT: A 127 LYS cc_start: 0.8308 (mttt) cc_final: 0.7985 (mttt) REVERT: A 183 PHE cc_start: 0.6929 (OUTLIER) cc_final: 0.6167 (m-80) REVERT: A 309 MET cc_start: 0.8193 (tpp) cc_final: 0.7677 (tpp) REVERT: A 405 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7963 (mm-30) REVERT: A 456 CYS cc_start: 0.8288 (m) cc_final: 0.7932 (p) REVERT: A 477 TYR cc_start: 0.7706 (OUTLIER) cc_final: 0.7243 (t80) REVERT: A 613 MET cc_start: 0.8954 (mmm) cc_final: 0.8172 (mtt) REVERT: A 624 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6622 (mt-10) REVERT: A 705 TRP cc_start: 0.8906 (t-100) cc_final: 0.8326 (t-100) REVERT: A 710 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7959 (mm110) REVERT: B 78 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7497 (mm-30) REVERT: B 127 LYS cc_start: 0.8312 (mttt) cc_final: 0.8049 (mttt) REVERT: B 183 PHE cc_start: 0.6647 (OUTLIER) cc_final: 0.5902 (m-80) REVERT: B 309 MET cc_start: 0.8189 (tpp) cc_final: 0.7687 (tpp) REVERT: B 405 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7949 (mm-30) REVERT: B 456 CYS cc_start: 0.8345 (m) cc_final: 0.8042 (p) REVERT: B 477 TYR cc_start: 0.7667 (OUTLIER) cc_final: 0.7178 (t80) REVERT: B 613 MET cc_start: 0.8948 (mmm) cc_final: 0.8196 (mtt) REVERT: B 624 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6640 (mt-10) REVERT: B 705 TRP cc_start: 0.8904 (t-100) cc_final: 0.8327 (t-100) REVERT: B 710 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7961 (mm110) outliers start: 42 outliers final: 26 residues processed: 241 average time/residue: 0.0820 time to fit residues: 31.6843 Evaluate side-chains 233 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 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 624 GLU Chi-restraints excluded: chain A residue 625 VAL 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 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 624 GLU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 710 GLN 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: 0.8980 chunk 37 optimal weight: 2.9990 chunk 75 optimal weight: 30.0000 chunk 94 optimal weight: 0.8980 chunk 118 optimal weight: 7.9990 chunk 82 optimal weight: 20.0000 chunk 69 optimal weight: 0.2980 chunk 132 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.182652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.131214 restraints weight = 24001.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.135668 restraints weight = 10629.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.138404 restraints weight = 6954.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.139881 restraints weight = 5605.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.140356 restraints weight = 5054.865| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2003 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= 0.126 Angle : 0.627 17.446 17152 Z= 0.313 Chirality : 0.042 0.203 1874 Planarity : 0.005 0.060 2142 Dihedral : 4.008 15.958 1658 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.00 % Allowed : 23.95 % Favored : 73.05 % 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: 1.20 (0.22), residues: 1484 helix: 1.96 (0.17), residues: 868 sheet: -1.16 (0.54), residues: 86 loop : -0.82 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 639 TYR 0.024 0.001 TYR A 770 PHE 0.027 0.001 PHE B 518 TRP 0.012 0.001 TRP A 397 HIS 0.006 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (12628) covalent geometry : angle 0.62632 / 0.31 (17132) SS BOND : bond 0.00246 / 0.12 ( 10) SS BOND : angle 1.25702 / 0.78 ( 20) hydrogen bonds : bond 0.03550 / 2.35 ( 720) hydrogen bonds : angle 4.31939 / 3.10 ( 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 248 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7519 (mm-30) REVERT: A 127 LYS cc_start: 0.8326 (mttt) cc_final: 0.7982 (mttt) REVERT: A 183 PHE cc_start: 0.6894 (OUTLIER) cc_final: 0.6140 (m-80) REVERT: A 196 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.6114 (t80) REVERT: A 309 MET cc_start: 0.8191 (tpp) cc_final: 0.7642 (tpp) REVERT: A 405 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7981 (mm-30) REVERT: A 456 CYS cc_start: 0.8312 (m) cc_final: 0.7964 (p) REVERT: A 477 TYR cc_start: 0.7685 (OUTLIER) cc_final: 0.7223 (t80) REVERT: A 613 MET cc_start: 0.8948 (mmm) cc_final: 0.8159 (mtt) REVERT: A 624 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6711 (mt-10) REVERT: A 655 HIS cc_start: 0.8571 (m90) cc_final: 0.7637 (m90) REVERT: A 710 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7896 (mm110) REVERT: B 78 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7512 (mm-30) REVERT: B 127 LYS cc_start: 0.8323 (mttt) cc_final: 0.8020 (mttt) REVERT: B 183 PHE cc_start: 0.6698 (OUTLIER) cc_final: 0.5836 (m-80) REVERT: B 196 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.6187 (t80) REVERT: B 405 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7952 (mm-30) REVERT: B 410 THR cc_start: 0.8297 (OUTLIER) cc_final: 0.8078 (m) REVERT: B 456 CYS cc_start: 0.8353 (m) cc_final: 0.8044 (p) REVERT: B 477 TYR cc_start: 0.7650 (OUTLIER) cc_final: 0.7163 (t80) REVERT: B 613 MET cc_start: 0.8966 (mmm) cc_final: 0.8186 (mtt) REVERT: B 624 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6717 (mt-10) REVERT: B 632 ASN cc_start: 0.8916 (t0) cc_final: 0.8447 (t0) REVERT: B 710 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7884 (mm110) outliers start: 40 outliers final: 26 residues processed: 238 average time/residue: 0.0839 time to fit residues: 32.1939 Evaluate side-chains 237 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 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 624 GLU Chi-restraints excluded: chain A residue 625 VAL 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 196 TYR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 410 THR 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 624 GLU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 710 GLN 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: 5.9990 chunk 4 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 2 optimal weight: 20.0000 chunk 104 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 125 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 30.0000 chunk 144 optimal weight: 7.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.180483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.128251 restraints weight = 24100.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.132605 restraints weight = 10783.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.135151 restraints weight = 7126.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.136625 restraints weight = 5805.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.136852 restraints weight = 5251.887| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12638 Z= 0.187 Angle : 0.664 16.586 17152 Z= 0.336 Chirality : 0.043 0.195 1874 Planarity : 0.005 0.059 2142 Dihedral : 4.192 16.032 1658 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.08 % Allowed : 23.87 % Favored : 73.05 % 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: 1.77 (0.17), residues: 870 sheet: -1.12 (0.53), residues: 88 loop : -0.78 (0.30), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 639 TYR 0.023 0.001 TYR B 138 PHE 0.024 0.002 PHE A 385 TRP 0.011 0.001 TRP B 397 HIS 0.009 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (12628) covalent geometry : angle 0.66342 / 0.34 (17132) SS BOND : bond 0.00306 / 0.15 ( 10) SS BOND : angle 1.28069 / 0.79 ( 20) hydrogen bonds : bond 0.03935 / 2.62 ( 720) hydrogen bonds : angle 4.38645 / 3.16 ( 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 247 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 206 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 LYS cc_start: 0.8341 (mttt) cc_final: 0.7959 (mttt) REVERT: A 183 PHE cc_start: 0.6717 (OUTLIER) cc_final: 0.5894 (m-80) REVERT: A 196 TYR cc_start: 0.7357 (OUTLIER) cc_final: 0.6022 (t80) REVERT: A 405 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7975 (mm-30) REVERT: A 477 TYR cc_start: 0.7678 (OUTLIER) cc_final: 0.7219 (t80) REVERT: A 613 MET cc_start: 0.9022 (mmm) cc_final: 0.8298 (mtt) REVERT: A 655 HIS cc_start: 0.8128 (m90) cc_final: 0.7903 (m90) REVERT: A 710 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8159 (mm-40) REVERT: B 127 LYS cc_start: 0.8344 (mttt) cc_final: 0.7972 (mttt) REVERT: B 183 PHE cc_start: 0.6751 (OUTLIER) cc_final: 0.5922 (m-80) REVERT: B 196 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.6145 (t80) REVERT: B 405 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7964 (mm-30) REVERT: B 477 TYR cc_start: 0.7681 (OUTLIER) cc_final: 0.7244 (t80) REVERT: B 632 ASN cc_start: 0.8833 (t0) cc_final: 0.8566 (t0) REVERT: B 655 HIS cc_start: 0.8495 (m90) cc_final: 0.8214 (m90) REVERT: B 710 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8283 (mm110) outliers start: 41 outliers final: 28 residues processed: 241 average time/residue: 0.0935 time to fit residues: 35.5193 Evaluate side-chains 229 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 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 624 GLU Chi-restraints excluded: chain A residue 625 VAL 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 196 TYR 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 624 GLU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 710 GLN 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: 9.9990 chunk 8 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 149 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.181725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.129977 restraints weight = 23729.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.134347 restraints weight = 10762.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.136988 restraints weight = 7120.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.138096 restraints weight = 5777.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.139040 restraints weight = 5269.262| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2175 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= 0.146 Angle : 0.667 16.924 17152 Z= 0.331 Chirality : 0.043 0.202 1874 Planarity : 0.005 0.058 2142 Dihedral : 4.144 16.345 1658 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.15 % Allowed : 24.77 % Favored : 72.07 % 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: 1.07 (0.22), residues: 1484 helix: 1.79 (0.17), residues: 870 sheet: -1.09 (0.54), residues: 88 loop : -0.79 (0.30), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 542 TYR 0.022 0.001 TYR B 138 PHE 0.023 0.001 PHE A 321 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 0.00341 / 0.15 (12628) covalent geometry : angle 0.66647 / 0.33 (17132) SS BOND : bond 0.00279 / 0.14 ( 10) SS BOND : angle 1.25583 / 0.78 ( 20) hydrogen bonds : bond 0.03759 / 2.51 ( 720) hydrogen bonds : angle 4.33224 / 3.11 ( 2106) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2524.58 seconds wall clock time: 44 minutes 15.01 seconds (2655.01 seconds total)