Starting phenix.real_space_refine on Thu Aug 6 07:09:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hgi_52135/08_2026/9hgi_52135.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hgi_52135/08_2026/9hgi_52135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hgi_52135/08_2026/9hgi_52135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hgi_52135/08_2026/9hgi_52135.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hgi_52135/08_2026/9hgi_52135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hgi_52135/08_2026/9hgi_52135.map" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 48 5.49 5 S 88 5.16 5 C 8504 2.51 5 N 2439 2.21 5 O 2578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 138 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13657 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6333 Classifications: {'peptide': 811} Link IDs: {'PTRANS': 46, 'TRANS': 764} Chain breaks: 1 Chain: "B" Number of atoms: 6340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 6340 Classifications: {'peptide': 812} Link IDs: {'PTRANS': 46, 'TRANS': 765} Chain breaks: 1 Chain: "C" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 498 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "D" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 486 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Time building chain proxies: 3.26, per 1000 atoms: 0.24 Number of scatterers: 13657 At special positions: 0 Unit cell: (116.45, 117.3, 105.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 P 48 15.00 O 2578 8.00 N 2439 7.00 C 8504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 570.4 milliseconds 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3022 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 10 sheets defined 53.9% alpha, 9.2% beta 24 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 20 through 38 Processing helix chain 'A' and resid 41 through 50 Proline residue: A 47 - end of helix Processing helix chain 'A' and resid 86 through 99 Processing helix chain 'A' and resid 115 through 123 removed outlier: 4.289A pdb=" N LEU A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 155 through 164 removed outlier: 5.616A pdb=" N HIS A 158 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY A 161 " --> pdb=" O HIS A 158 " (cutoff:3.500A) Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 175 through 182 removed outlier: 3.530A pdb=" N GLN A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 190 through 205 Processing helix chain 'A' and resid 216 through 228 Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.817A pdb=" N SER A 245 " --> pdb=" O PRO A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 264 removed outlier: 3.605A pdb=" N ALA A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 296 Processing helix chain 'A' and resid 306 through 321 removed outlier: 3.565A pdb=" N ILE A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 342 removed outlier: 4.099A pdb=" N GLY A 340 " --> pdb=" O THR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 377 through 387 removed outlier: 3.500A pdb=" N ARG A 387 " --> pdb=" O GLN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 422 Processing helix chain 'A' and resid 458 through 474 removed outlier: 5.021A pdb=" N TYR A 466 " --> pdb=" O ASN A 462 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LYS A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 492 Processing helix chain 'A' and resid 506 through 531 removed outlier: 3.669A pdb=" N GLN A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG A 526 " --> pdb=" O LEU A 522 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.514A pdb=" N ALA A 545 " --> pdb=" O PRO A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 558 Processing helix chain 'A' and resid 563 through 574 Processing helix chain 'A' and resid 576 through 595 Processing helix chain 'A' and resid 596 through 600 Processing helix chain 'A' and resid 601 through 613 Processing helix chain 'A' and resid 637 through 654 Processing helix chain 'A' and resid 668 through 677 Processing helix chain 'A' and resid 679 through 692 Processing helix chain 'A' and resid 702 through 716 Processing helix chain 'A' and resid 723 through 741 Processing helix chain 'A' and resid 756 through 760 Processing helix chain 'A' and resid 761 through 772 removed outlier: 3.571A pdb=" N HIS A 772 " --> pdb=" O LEU A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 793 Processing helix chain 'A' and resid 794 through 797 Processing helix chain 'A' and resid 822 through 834 Processing helix chain 'B' and resid 20 through 38 Processing helix chain 'B' and resid 41 through 50 Proline residue: B 47 - end of helix Processing helix chain 'B' and resid 86 through 99 Processing helix chain 'B' and resid 111 through 115 removed outlier: 4.065A pdb=" N PHE B 115 " --> pdb=" O ARG B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 123 Processing helix chain 'B' and resid 124 through 127 Processing helix chain 'B' and resid 139 through 144 Processing helix chain 'B' and resid 155 through 157 No H-bonds generated for 'chain 'B' and resid 155 through 157' Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 175 through 181 Processing helix chain 'B' and resid 182 through 185 Processing helix chain 'B' and resid 190 through 205 Processing helix chain 'B' and resid 216 through 228 Processing helix chain 'B' and resid 256 through 265 Processing helix chain 'B' and resid 285 through 296 Processing helix chain 'B' and resid 306 through 321 removed outlier: 3.805A pdb=" N ILE B 312 " --> pdb=" O SER B 308 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN B 319 " --> pdb=" O ARG B 315 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE B 320 " --> pdb=" O PHE B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 342 removed outlier: 4.109A pdb=" N GLY B 340 " --> pdb=" O THR B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.836A pdb=" N VAL B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 386 Processing helix chain 'B' and resid 412 through 422 Processing helix chain 'B' and resid 458 through 474 removed outlier: 5.011A pdb=" N TYR B 466 " --> pdb=" O ASN B 462 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LYS B 467 " --> pdb=" O LYS B 463 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 491 Processing helix chain 'B' and resid 506 through 531 removed outlier: 3.655A pdb=" N GLN B 525 " --> pdb=" O ALA B 521 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ARG B 526 " --> pdb=" O LEU B 522 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASP B 527 " --> pdb=" O ARG B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 546 removed outlier: 3.587A pdb=" N GLN B 543 " --> pdb=" O SER B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 558 Processing helix chain 'B' and resid 563 through 574 Processing helix chain 'B' and resid 576 through 595 Processing helix chain 'B' and resid 596 through 600 Processing helix chain 'B' and resid 601 through 613 Processing helix chain 'B' and resid 637 through 654 removed outlier: 3.618A pdb=" N MET B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 677 removed outlier: 3.540A pdb=" N LEU B 673 " --> pdb=" O PRO B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 692 Processing helix chain 'B' and resid 698 through 701 removed outlier: 3.584A pdb=" N LEU B 701 " --> pdb=" O GLY B 698 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 698 through 701' Processing helix chain 'B' and resid 702 through 715 Processing helix chain 'B' and resid 723 through 740 Processing helix chain 'B' and resid 756 through 760 Processing helix chain 'B' and resid 761 through 770 Processing helix chain 'B' and resid 771 through 774 Processing helix chain 'B' and resid 781 through 797 removed outlier: 3.571A pdb=" N LEU B 785 " --> pdb=" O THR B 781 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU B 788 " --> pdb=" O GLN B 784 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 789 " --> pdb=" O LEU B 785 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA B 791 " --> pdb=" O ALA B 787 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ARG B 794 " --> pdb=" O MET B 790 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLU B 795 " --> pdb=" O ALA B 791 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE B 796 " --> pdb=" O HIS B 792 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 797 " --> pdb=" O LYS B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 834 Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 58 removed outlier: 3.680A pdb=" N THR A 54 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 76 " --> pdb=" O HIS A 233 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL A 235 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL A 78 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N GLY A 237 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG A 80 " --> pdb=" O GLY A 237 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU A 107 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ASP A 174 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL A 109 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 324 through 327 removed outlier: 6.426A pdb=" N LEU A 325 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ARG A 248 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE A 398 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 250 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N MET A 400 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 615 through 620 Processing sheet with id=AA4, first strand: chain 'A' and resid 656 through 657 Processing sheet with id=AA5, first strand: chain 'A' and resid 743 through 746 Processing sheet with id=AA6, first strand: chain 'B' and resid 54 through 58 removed outlier: 6.812A pdb=" N THR B 54 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL B 236 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLU B 56 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL B 76 " --> pdb=" O HIS B 233 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL B 235 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL B 78 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N GLY B 237 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ARG B 80 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU B 107 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ASP B 174 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL B 109 " --> pdb=" O ASP B 174 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 324 through 327 removed outlier: 6.242A pdb=" N ARG B 248 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE B 398 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU B 250 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N MET B 400 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 615 through 620 Processing sheet with id=AA9, first strand: chain 'B' and resid 656 through 657 Processing sheet with id=AB1, first strand: chain 'B' and resid 743 through 746 626 hydrogen bonds defined for protein. 1758 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2195 1.31 - 1.44: 3952 1.44 - 1.57: 7692 1.57 - 1.69: 96 1.69 - 1.82: 134 Bond restraints: 14069 Sorted by residual: bond pdb=" C GLY A 615 " pdb=" O GLY A 615 " ideal model delta sigma weight residual 1.236 1.199 0.036 5.30e-03 3.56e+04 4.73e+01 bond pdb=" NE ARG A 813 " pdb=" CZ ARG A 813 " ideal model delta sigma weight residual 1.326 1.253 0.073 1.10e-02 8.26e+03 4.43e+01 bond pdb=" NE ARG A 594 " pdb=" CZ ARG A 594 " ideal model delta sigma weight residual 1.326 1.258 0.068 1.10e-02 8.26e+03 3.87e+01 bond pdb=" NE ARG B 594 " pdb=" CZ ARG B 594 " ideal model delta sigma weight residual 1.326 1.258 0.068 1.10e-02 8.26e+03 3.78e+01 bond pdb=" C GLY B 615 " pdb=" O GLY B 615 " ideal model delta sigma weight residual 1.237 1.201 0.036 7.00e-03 2.04e+04 2.65e+01 ... (remaining 14064 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.42: 18948 4.42 - 8.84: 350 8.84 - 13.26: 22 13.26 - 17.67: 2 17.67 - 22.09: 2 Bond angle restraints: 19324 Sorted by residual: angle pdb=" N PRO B 840 " pdb=" CA PRO B 840 " pdb=" C PRO B 840 " ideal model delta sigma weight residual 112.47 90.38 22.09 2.06e+00 2.36e-01 1.15e+02 angle pdb=" N PRO A 840 " pdb=" CA PRO A 840 " pdb=" C PRO A 840 " ideal model delta sigma weight residual 112.47 91.59 20.88 2.06e+00 2.36e-01 1.03e+02 angle pdb=" O4' DA C 40 " pdb=" C1' DA C 40 " pdb=" N9 DA C 40 " ideal model delta sigma weight residual 108.00 113.82 -5.82 7.00e-01 2.04e+00 6.91e+01 angle pdb=" O4' DA D 40 " pdb=" C1' DA D 40 " pdb=" N9 DA D 40 " ideal model delta sigma weight residual 108.00 113.62 -5.62 7.00e-01 2.04e+00 6.46e+01 angle pdb=" C PRO B 840 " pdb=" CA PRO B 840 " pdb=" CB PRO B 840 " ideal model delta sigma weight residual 111.56 124.61 -13.05 1.65e+00 3.67e-01 6.25e+01 ... (remaining 19319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 7973 35.99 - 71.98: 302 71.98 - 107.97: 20 107.97 - 143.97: 0 143.97 - 179.96: 1 Dihedral angle restraints: 8296 sinusoidal: 3609 harmonic: 4687 Sorted by residual: dihedral pdb=" CA SER B 114 " pdb=" C SER B 114 " pdb=" N PHE B 115 " pdb=" CA PHE B 115 " ideal model delta harmonic sigma weight residual 180.00 -150.20 -29.80 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" N TRP B 839 " pdb=" C TRP B 839 " pdb=" CA TRP B 839 " pdb=" CB TRP B 839 " ideal model delta harmonic sigma weight residual 122.80 137.52 -14.72 0 2.50e+00 1.60e-01 3.46e+01 dihedral pdb=" CA ALA B 538 " pdb=" C ALA B 538 " pdb=" N SER B 539 " pdb=" CA SER B 539 " ideal model delta harmonic sigma weight residual 180.00 151.36 28.64 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 8293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 1817 0.131 - 0.262: 341 0.262 - 0.394: 33 0.394 - 0.525: 2 0.525 - 0.656: 3 Chirality restraints: 2196 Sorted by residual: chirality pdb=" P DA D 19 " pdb=" OP1 DA D 19 " pdb=" OP2 DA D 19 " pdb=" O5' DA D 19 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" P DT C 39 " pdb=" OP1 DT C 39 " pdb=" OP2 DT C 39 " pdb=" O5' DT C 39 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CA TRP B 839 " pdb=" N TRP B 839 " pdb=" C TRP B 839 " pdb=" CB TRP B 839 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.54e+00 ... (remaining 2193 not shown) Planarity restraints: 2325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 839 " -0.137 2.00e-02 2.50e+03 6.92e-02 1.20e+02 pdb=" CG TRP B 839 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP B 839 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 839 " 0.072 2.00e-02 2.50e+03 pdb=" NE1 TRP B 839 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP B 839 " 0.019 2.00e-02 2.50e+03 pdb=" CE3 TRP B 839 " 0.068 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 839 " -0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 839 " 0.040 2.00e-02 2.50e+03 pdb=" CH2 TRP B 839 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 839 " 0.121 2.00e-02 2.50e+03 5.98e-02 8.95e+01 pdb=" CG TRP A 839 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP A 839 " -0.039 2.00e-02 2.50e+03 pdb=" CD2 TRP A 839 " -0.040 2.00e-02 2.50e+03 pdb=" NE1 TRP A 839 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP A 839 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP A 839 " -0.062 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 839 " 0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 839 " -0.050 2.00e-02 2.50e+03 pdb=" CH2 TRP A 839 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 38 " -0.104 2.00e-02 2.50e+03 5.43e-02 5.90e+01 pdb=" CG TYR B 38 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR B 38 " 0.054 2.00e-02 2.50e+03 pdb=" CD2 TYR B 38 " 0.056 2.00e-02 2.50e+03 pdb=" CE1 TYR B 38 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR B 38 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 38 " -0.036 2.00e-02 2.50e+03 pdb=" OH TYR B 38 " -0.051 2.00e-02 2.50e+03 ... (remaining 2322 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 12 2.44 - 3.06: 8356 3.06 - 3.67: 20249 3.67 - 4.29: 31551 4.29 - 4.90: 50999 Nonbonded interactions: 111167 Sorted by model distance: nonbonded pdb=" NE ARG B 495 " pdb=" NH2 ARG B 497 " model vdw 1.830 3.200 nonbonded pdb=" CZ ARG B 495 " pdb=" NH2 ARG B 497 " model vdw 2.177 3.350 nonbonded pdb=" O TRP B 839 " pdb=" N MET B 841 " model vdw 2.263 3.120 nonbonded pdb=" OD2 ASP A 824 " pdb=" NH2 ARG B 607 " model vdw 2.318 3.120 nonbonded pdb=" O TRP A 839 " pdb=" N MET A 841 " model vdw 2.339 3.120 ... (remaining 111162 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 16 through 433 or resid 451 through 843)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.370 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9179 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 : 0.012 0.104 14069 Z= 0.742 Angle : 1.667 22.093 19324 Z= 1.095 Chirality : 0.102 0.656 2196 Planarity : 0.018 0.186 2325 Dihedral : 16.696 179.957 5274 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.23 % Favored : 97.65 % Rotamer: Outliers : 0.22 % Allowed : 3.20 % Favored : 96.59 % Cbeta Deviations : 0.33 % 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: -0.87 (0.19), residues: 1615 helix: -1.01 (0.16), residues: 780 sheet: 0.73 (0.33), residues: 208 loop : -0.17 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.004 ARG A 149 TYR 0.104 0.015 TYR B 38 PHE 0.059 0.011 PHE A 411 TRP 0.137 0.020 TRP B 839 HIS 0.026 0.005 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.01176 / 0.74 (14069) covalent geometry : angle 1.66733 / 1.10 (19324) hydrogen bonds : bond 0.17505 / 11.60 ( 686) hydrogen bonds : angle 7.03135 / 5.04 ( 1878) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 172 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.9221 (p0) cc_final: 0.8814 (t0) REVERT: A 63 VAL cc_start: 0.9408 (m) cc_final: 0.9163 (p) REVERT: A 64 THR cc_start: 0.9432 (m) cc_final: 0.9205 (p) REVERT: A 164 LEU cc_start: 0.8882 (mt) cc_final: 0.8652 (mm) REVERT: A 177 MET cc_start: 0.9476 (mmm) cc_final: 0.9228 (mmt) REVERT: A 355 LEU cc_start: 0.9100 (mt) cc_final: 0.8891 (pt) REVERT: A 535 ASP cc_start: 0.8518 (m-30) cc_final: 0.8246 (p0) REVERT: A 685 GLN cc_start: 0.9319 (tp40) cc_final: 0.9035 (tt0) REVERT: B 65 PHE cc_start: 0.9258 (m-10) cc_final: 0.8993 (m-10) REVERT: B 112 ARG cc_start: 0.8683 (mtt180) cc_final: 0.8483 (mtt90) REVERT: B 131 PHE cc_start: 0.8276 (p90) cc_final: 0.8026 (p90) REVERT: B 578 MET cc_start: 0.9157 (ttp) cc_final: 0.8937 (tpt) REVERT: B 790 MET cc_start: 0.4587 (mmm) cc_final: 0.3747 (ptm) outliers start: 3 outliers final: 3 residues processed: 174 average time/residue: 0.8402 time to fit residues: 156.5111 Evaluate side-chains 105 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain B residue 377 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.0070 chunk 149 optimal weight: 0.6980 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN A 727 HIS A 749 GLN B 100 HIS B 143 ASN B 167 ASN B 486 HIS B 727 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.122022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.075003 restraints weight = 24670.518| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.21 r_work: 0.2754 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14069 Z= 0.164 Angle : 0.736 11.403 19324 Z= 0.389 Chirality : 0.049 0.255 2196 Planarity : 0.005 0.063 2325 Dihedral : 18.486 179.021 2325 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.45 % Allowed : 8.93 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.87 (0.21), residues: 1615 helix: 0.86 (0.18), residues: 780 sheet: 0.81 (0.33), residues: 215 loop : 0.34 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 159 TYR 0.016 0.002 TYR B 786 PHE 0.024 0.002 PHE B 732 TRP 0.029 0.002 TRP B 839 HIS 0.007 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (14069) covalent geometry : angle 0.73557 / 0.39 (19324) hydrogen bonds : bond 0.05363 / 3.73 ( 686) hydrogen bonds : angle 4.68472 / 3.35 ( 1878) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 60 HIS cc_start: 0.9005 (OUTLIER) cc_final: 0.8722 (m90) REVERT: A 64 THR cc_start: 0.9294 (m) cc_final: 0.9054 (p) REVERT: A 355 LEU cc_start: 0.8891 (mt) cc_final: 0.8521 (pt) REVERT: A 389 ARG cc_start: 0.8624 (mtm110) cc_final: 0.8277 (mtm110) REVERT: B 131 PHE cc_start: 0.7585 (p90) cc_final: 0.7293 (p90) REVERT: B 790 MET cc_start: 0.5020 (mmm) cc_final: 0.3688 (ptm) REVERT: B 842 MET cc_start: 0.7859 (mpt) cc_final: 0.7260 (tmt) outliers start: 20 outliers final: 6 residues processed: 121 average time/residue: 0.5574 time to fit residues: 73.6260 Evaluate side-chains 99 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 841 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 111 optimal weight: 0.2980 chunk 48 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 141 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 HIS A 233 HIS B 50 HIS B 100 HIS ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 749 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.122191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.072664 restraints weight = 24573.134| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.36 r_work: 0.2816 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14069 Z= 0.142 Angle : 0.634 8.658 19324 Z= 0.336 Chirality : 0.045 0.246 2196 Planarity : 0.005 0.063 2325 Dihedral : 18.370 177.079 2321 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.03 % Allowed : 9.37 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.21), residues: 1615 helix: 1.34 (0.18), residues: 789 sheet: 0.89 (0.34), residues: 217 loop : 0.48 (0.27), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 193 TYR 0.022 0.002 TYR A 239 PHE 0.022 0.001 PHE A 732 TRP 0.016 0.001 TRP B 839 HIS 0.005 0.001 HIS B 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (14069) covalent geometry : angle 0.63362 / 0.34 (19324) hydrogen bonds : bond 0.04418 / 3.04 ( 686) hydrogen bonds : angle 4.36411 / 3.13 ( 1878) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 HIS cc_start: 0.9009 (OUTLIER) cc_final: 0.8726 (m90) REVERT: A 230 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.9060 (ptpp) REVERT: A 355 LEU cc_start: 0.8796 (mt) cc_final: 0.8393 (pt) REVERT: A 389 ARG cc_start: 0.8554 (mtm110) cc_final: 0.8190 (mtm110) REVERT: B 131 PHE cc_start: 0.7617 (p90) cc_final: 0.7342 (p90) REVERT: B 155 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8246 (tm-30) REVERT: B 395 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7302 (mt-10) REVERT: B 527 ASP cc_start: 0.8911 (m-30) cc_final: 0.8645 (m-30) REVERT: B 682 ARG cc_start: 0.8699 (mtp180) cc_final: 0.8444 (mpp-170) REVERT: B 790 MET cc_start: 0.4997 (mmm) cc_final: 0.4540 (mtm) REVERT: B 804 ARG cc_start: 0.8357 (mtt-85) cc_final: 0.8110 (ttm-80) REVERT: B 842 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7169 (tmt) outliers start: 28 outliers final: 8 residues processed: 116 average time/residue: 0.6356 time to fit residues: 80.8169 Evaluate side-chains 98 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 749 GLN Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 57 optimal weight: 0.5980 chunk 12 optimal weight: 9.9990 chunk 49 optimal weight: 0.5980 chunk 92 optimal weight: 7.9990 chunk 115 optimal weight: 0.0770 chunk 37 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 100 HIS B 163 ASN B 261 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.120521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.072541 restraints weight = 24672.651| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.27 r_work: 0.2767 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14069 Z= 0.131 Angle : 0.610 9.466 19324 Z= 0.319 Chirality : 0.044 0.259 2196 Planarity : 0.004 0.047 2325 Dihedral : 18.216 175.530 2321 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.67 % Allowed : 10.53 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.21), residues: 1615 helix: 1.58 (0.18), residues: 777 sheet: 0.89 (0.34), residues: 219 loop : 0.45 (0.27), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 112 TYR 0.014 0.002 TYR A 382 PHE 0.020 0.001 PHE A 732 TRP 0.013 0.001 TRP B 839 HIS 0.013 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (14069) covalent geometry : angle 0.60952 / 0.32 (19324) hydrogen bonds : bond 0.04049 / 2.79 ( 686) hydrogen bonds : angle 4.23487 / 3.04 ( 1878) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 230 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.9079 (ptpp) REVERT: A 389 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8142 (mtm110) REVERT: B 131 PHE cc_start: 0.7619 (p90) cc_final: 0.7382 (p90) REVERT: B 155 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8332 (tp30) REVERT: B 195 ASP cc_start: 0.9270 (m-30) cc_final: 0.9026 (t0) REVERT: B 395 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7349 (mt-10) REVERT: B 682 ARG cc_start: 0.8686 (mtp180) cc_final: 0.8456 (mpp-170) REVERT: B 790 MET cc_start: 0.5133 (mmm) cc_final: 0.4642 (mtm) REVERT: B 842 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7183 (tmt) outliers start: 23 outliers final: 7 residues processed: 107 average time/residue: 0.5980 time to fit residues: 70.6954 Evaluate side-chains 92 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 45 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 chunk 126 optimal weight: 2.9990 chunk 158 optimal weight: 0.0980 chunk 88 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 100 HIS B 233 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.119926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.071757 restraints weight = 24872.608| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.27 r_work: 0.2764 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14069 Z= 0.150 Angle : 0.608 9.653 19324 Z= 0.315 Chirality : 0.044 0.253 2196 Planarity : 0.004 0.069 2325 Dihedral : 18.105 175.170 2321 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.38 % Allowed : 10.89 % Favored : 87.73 % 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: 1.58 (0.21), residues: 1615 helix: 1.68 (0.18), residues: 786 sheet: 0.95 (0.35), residues: 217 loop : 0.40 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 112 TYR 0.015 0.002 TYR A 786 PHE 0.020 0.001 PHE A 732 TRP 0.011 0.001 TRP B 839 HIS 0.015 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (14069) covalent geometry : angle 0.60817 / 0.31 (19324) hydrogen bonds : bond 0.04030 / 2.77 ( 686) hydrogen bonds : angle 4.15333 / 2.99 ( 1878) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.9073 (ptpp) REVERT: A 389 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8066 (mtm110) REVERT: A 820 ASN cc_start: 0.8842 (p0) cc_final: 0.8602 (p0) REVERT: B 131 PHE cc_start: 0.7617 (p90) cc_final: 0.7415 (p90) REVERT: B 155 GLU cc_start: 0.9105 (tt0) cc_final: 0.8271 (tp30) REVERT: B 395 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7153 (pt0) REVERT: B 682 ARG cc_start: 0.8692 (mtp180) cc_final: 0.8471 (mpp-170) REVERT: B 790 MET cc_start: 0.5205 (mmm) cc_final: 0.4742 (mtm) REVERT: B 804 ARG cc_start: 0.8481 (mtt-85) cc_final: 0.8205 (ttm-80) REVERT: B 842 MET cc_start: 0.7651 (mpt) cc_final: 0.7211 (tmt) outliers start: 19 outliers final: 7 residues processed: 99 average time/residue: 0.6340 time to fit residues: 68.8022 Evaluate side-chains 93 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 626 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 154 optimal weight: 20.0000 chunk 31 optimal weight: 0.7980 chunk 106 optimal weight: 20.0000 chunk 44 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 100 HIS B 501 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.119981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.071902 restraints weight = 25011.077| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.30 r_work: 0.2765 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14069 Z= 0.146 Angle : 0.600 10.736 19324 Z= 0.309 Chirality : 0.043 0.250 2196 Planarity : 0.005 0.124 2325 Dihedral : 17.994 175.806 2321 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.82 % Allowed : 11.04 % Favored : 87.15 % 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: 1.63 (0.21), residues: 1615 helix: 1.76 (0.18), residues: 786 sheet: 1.00 (0.35), residues: 217 loop : 0.34 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 112 TYR 0.020 0.002 TYR A 239 PHE 0.019 0.001 PHE A 732 TRP 0.011 0.001 TRP A 839 HIS 0.015 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (14069) covalent geometry : angle 0.59982 / 0.31 (19324) hydrogen bonds : bond 0.03919 / 2.69 ( 686) hydrogen bonds : angle 4.13288 / 2.97 ( 1878) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: A 60 HIS cc_start: 0.9031 (OUTLIER) cc_final: 0.8820 (m90) REVERT: A 159 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7887 (ttp80) REVERT: A 230 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.9093 (ptpp) REVERT: A 389 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8134 (mtm110) REVERT: A 820 ASN cc_start: 0.8847 (p0) cc_final: 0.8634 (p0) REVERT: B 155 GLU cc_start: 0.9111 (tt0) cc_final: 0.8243 (tp30) REVERT: B 195 ASP cc_start: 0.9194 (m-30) cc_final: 0.8973 (t0) REVERT: B 395 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7231 (pt0) REVERT: B 400 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.9035 (mmm) REVERT: B 790 MET cc_start: 0.5205 (mmm) cc_final: 0.4766 (mtm) REVERT: B 842 MET cc_start: 0.7575 (mpt) cc_final: 0.7226 (tmt) outliers start: 25 outliers final: 8 residues processed: 107 average time/residue: 0.5274 time to fit residues: 62.1643 Evaluate side-chains 97 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 159 ARG Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 400 MET Chi-restraints excluded: chain B residue 626 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 15 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 0.0470 chunk 109 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 HIS B 100 HIS B 679 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.120688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.074297 restraints weight = 24958.765| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.22 r_work: 0.2734 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14069 Z= 0.134 Angle : 0.595 11.869 19324 Z= 0.305 Chirality : 0.043 0.248 2196 Planarity : 0.007 0.220 2325 Dihedral : 17.938 177.262 2321 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.60 % Allowed : 11.62 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.66 (0.22), residues: 1615 helix: 1.80 (0.18), residues: 788 sheet: 1.02 (0.35), residues: 217 loop : 0.32 (0.27), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 112 TYR 0.014 0.001 TYR A 786 PHE 0.021 0.001 PHE B 688 TRP 0.010 0.001 TRP A 839 HIS 0.010 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (14069) covalent geometry : angle 0.59496 / 0.31 (19324) hydrogen bonds : bond 0.03773 / 2.58 ( 686) hydrogen bonds : angle 4.08921 / 2.94 ( 1878) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 230 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.9089 (ptpp) REVERT: A 389 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8104 (mtm110) REVERT: A 820 ASN cc_start: 0.8809 (p0) cc_final: 0.8538 (p0) REVERT: B 155 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8064 (tp30) REVERT: B 195 ASP cc_start: 0.9189 (m-30) cc_final: 0.8967 (t0) REVERT: B 395 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7079 (pt0) REVERT: B 400 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8935 (mmm) REVERT: B 487 MET cc_start: 0.9125 (tpt) cc_final: 0.8904 (tpp) REVERT: B 708 ARG cc_start: 0.7137 (ttp80) cc_final: 0.6862 (ttp80) REVERT: B 790 MET cc_start: 0.5326 (mmm) cc_final: 0.4874 (mtm) REVERT: B 842 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7159 (tmt) outliers start: 22 outliers final: 9 residues processed: 100 average time/residue: 0.6400 time to fit residues: 70.3188 Evaluate side-chains 98 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 400 MET Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 39 optimal weight: 0.0030 chunk 21 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 146 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 149 optimal weight: 0.4980 chunk 103 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.120997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.074812 restraints weight = 24934.109| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.19 r_work: 0.2765 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14069 Z= 0.123 Angle : 0.590 12.693 19324 Z= 0.301 Chirality : 0.042 0.245 2196 Planarity : 0.006 0.192 2325 Dihedral : 17.848 179.676 2321 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.60 % Allowed : 11.55 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.22), residues: 1615 helix: 1.89 (0.18), residues: 788 sheet: 1.08 (0.35), residues: 216 loop : 0.34 (0.28), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 112 TYR 0.022 0.001 TYR A 239 PHE 0.019 0.001 PHE B 732 TRP 0.009 0.001 TRP A 839 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (14069) covalent geometry : angle 0.59000 / 0.30 (19324) hydrogen bonds : bond 0.03620 / 2.47 ( 686) hydrogen bonds : angle 4.03506 / 2.90 ( 1878) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 230 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9096 (ptpp) REVERT: A 389 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8099 (mtm110) REVERT: A 770 ASP cc_start: 0.9194 (m-30) cc_final: 0.8860 (p0) REVERT: A 820 ASN cc_start: 0.8809 (p0) cc_final: 0.8535 (p0) REVERT: B 195 ASP cc_start: 0.9169 (m-30) cc_final: 0.8967 (t0) REVERT: B 395 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7147 (pt0) REVERT: B 400 MET cc_start: 0.9212 (OUTLIER) cc_final: 0.8978 (mmm) REVERT: B 487 MET cc_start: 0.9154 (tpt) cc_final: 0.8945 (tpp) REVERT: B 708 ARG cc_start: 0.7199 (ttp80) cc_final: 0.6766 (ttp80) REVERT: B 790 MET cc_start: 0.5368 (mmm) cc_final: 0.4910 (mtm) REVERT: B 842 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7160 (tmt) outliers start: 22 outliers final: 8 residues processed: 103 average time/residue: 0.5281 time to fit residues: 59.8181 Evaluate side-chains 96 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 400 MET Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 118 optimal weight: 0.0370 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 chunk 162 optimal weight: 30.0000 chunk 8 optimal weight: 0.3980 chunk 60 optimal weight: 0.0370 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.122104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.075943 restraints weight = 24959.294| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.20 r_work: 0.2785 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14069 Z= 0.110 Angle : 0.583 13.509 19324 Z= 0.297 Chirality : 0.041 0.240 2196 Planarity : 0.005 0.161 2325 Dihedral : 17.696 176.140 2321 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.09 % Allowed : 12.35 % Favored : 86.56 % 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: 1.85 (0.22), residues: 1615 helix: 1.98 (0.18), residues: 788 sheet: 1.13 (0.35), residues: 216 loop : 0.37 (0.28), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 112 TYR 0.016 0.001 TYR A 786 PHE 0.030 0.001 PHE B 131 TRP 0.008 0.001 TRP B 499 HIS 0.003 0.000 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (14069) covalent geometry : angle 0.58253 / 0.30 (19324) hydrogen bonds : bond 0.03380 / 2.31 ( 686) hydrogen bonds : angle 3.96386 / 2.86 ( 1878) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 174 ASP cc_start: 0.8728 (t70) cc_final: 0.8513 (t0) REVERT: A 230 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.9091 (ptpp) REVERT: A 389 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8110 (mtm110) REVERT: A 770 ASP cc_start: 0.9198 (m-30) cc_final: 0.8867 (p0) REVERT: B 131 PHE cc_start: 0.7621 (p90) cc_final: 0.7401 (p90) REVERT: B 682 ARG cc_start: 0.8633 (mmm-85) cc_final: 0.8327 (mpp-170) REVERT: B 708 ARG cc_start: 0.7175 (ttp80) cc_final: 0.6636 (ttp80) REVERT: B 790 MET cc_start: 0.5360 (mmm) cc_final: 0.4889 (mtm) REVERT: B 842 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.7230 (tmm) outliers start: 15 outliers final: 3 residues processed: 98 average time/residue: 0.5816 time to fit residues: 62.5620 Evaluate side-chains 91 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.0570 chunk 85 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 159 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 163 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 = 0.3806 r_free = 0.3806 target = 0.120143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.073759 restraints weight = 24836.333| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.17 r_work: 0.2749 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14069 Z= 0.175 Angle : 0.621 13.880 19324 Z= 0.313 Chirality : 0.043 0.234 2196 Planarity : 0.006 0.153 2325 Dihedral : 17.647 175.314 2319 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.80 % Allowed : 12.78 % Favored : 86.42 % 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: 1.77 (0.22), residues: 1615 helix: 1.94 (0.19), residues: 788 sheet: 0.96 (0.34), residues: 223 loop : 0.34 (0.28), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 112 TYR 0.023 0.002 TYR A 239 PHE 0.032 0.001 PHE B 131 TRP 0.011 0.001 TRP B 499 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (14069) covalent geometry : angle 0.62073 / 0.31 (19324) hydrogen bonds : bond 0.03829 / 2.60 ( 686) hydrogen bonds : angle 4.01004 / 2.89 ( 1878) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 230 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.9100 (ptpp) REVERT: A 389 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8105 (mtm110) REVERT: A 770 ASP cc_start: 0.9181 (m-30) cc_final: 0.8841 (p0) REVERT: B 131 PHE cc_start: 0.7583 (p90) cc_final: 0.7356 (p90) REVERT: B 142 MET cc_start: 0.7330 (ptt) cc_final: 0.6546 (pmm) REVERT: B 147 PHE cc_start: 0.7220 (m-80) cc_final: 0.6913 (m-80) REVERT: B 195 ASP cc_start: 0.8604 (t0) cc_final: 0.8273 (t0) REVERT: B 395 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7162 (pt0) REVERT: B 400 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8989 (mmm) REVERT: B 682 ARG cc_start: 0.8641 (mmm-85) cc_final: 0.8342 (mpp-170) REVERT: B 708 ARG cc_start: 0.7102 (ttp80) cc_final: 0.6669 (ttp80) REVERT: B 790 MET cc_start: 0.5460 (mmm) cc_final: 0.4974 (mtm) REVERT: B 842 MET cc_start: 0.7541 (mpt) cc_final: 0.7206 (tmt) outliers start: 11 outliers final: 7 residues processed: 94 average time/residue: 0.6478 time to fit residues: 66.9209 Evaluate side-chains 95 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 400 MET Chi-restraints excluded: chain B residue 626 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 160 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 26 optimal weight: 0.0270 chunk 143 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 chunk 112 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 85 optimal weight: 0.0270 chunk 54 optimal weight: 0.6980 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 163 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 = 0.3828 r_free = 0.3828 target = 0.121878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.075418 restraints weight = 25176.741| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.23 r_work: 0.2803 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14069 Z= 0.107 Angle : 0.589 13.921 19324 Z= 0.296 Chirality : 0.041 0.239 2196 Planarity : 0.005 0.121 2325 Dihedral : 17.510 173.132 2319 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.80 % Allowed : 12.85 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.22), residues: 1615 helix: 2.02 (0.19), residues: 788 sheet: 1.08 (0.35), residues: 223 loop : 0.33 (0.28), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 112 TYR 0.016 0.001 TYR A 786 PHE 0.032 0.001 PHE B 131 TRP 0.010 0.001 TRP B 839 HIS 0.002 0.000 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (14069) covalent geometry : angle 0.58913 / 0.30 (19324) hydrogen bonds : bond 0.03297 / 2.26 ( 686) hydrogen bonds : angle 3.93043 / 2.85 ( 1878) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4445.86 seconds wall clock time: 76 minutes 31.57 seconds (4591.57 seconds total)