Starting phenix.real_space_refine on Sat Sep 12 08:33:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v99_31811/09_2026/7v99_31811.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v99_31811/09_2026/7v99_31811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7v99_31811/09_2026/7v99_31811.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v99_31811/09_2026/7v99_31811.cif" model { file = "/net/cci-nas-00/data/ceres_data/7v99_31811/09_2026/7v99_31811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v99_31811/09_2026/7v99_31811.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v99_31811/09_2026/7v99_31811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v99_31811/09_2026/7v99_31811.map" } resolution = 3.54 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= 0.008 sd= 0.242 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 249 5.49 5 S 39 5.16 5 C 8291 2.51 5 N 2662 2.21 5 O 3341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14582 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7898 Classifications: {'peptide': 991} Link IDs: {'PTRANS': 62, 'TRANS': 928} Chain breaks: 1 Chain: "K" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 668 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "L" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "R" Number of atoms: 5156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 5156 Classifications: {'RNAv2': 243} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 9, 'rna3p_pur': 105, 'rna3p_pyr': 123} Link IDs: {'rna2p': 15, 'rna3p': 227} Chain breaks: 2 Chain: "S" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 127 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Time building chain proxies: 3.57, per 1000 atoms: 0.24 Number of scatterers: 14582 At special positions: 0 Unit cell: (148.5, 125.4, 132, 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 39 16.00 P 249 15.00 O 3341 8.00 N 2662 7.00 C 8291 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 845 " - pdb=" SG CYS A 896 " distance=2.05 Simple disulfide: pdb=" SG CYS A 982 " - pdb=" SG CYS A1043 " distance=2.05 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: 1.27 Conformation dependent library (CDL) restraints added in 585.9 milliseconds 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 11 sheets defined 57.2% alpha, 9.1% beta 53 base pairs and 118 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 4 through 18 removed outlier: 3.783A pdb=" N LEU A 13 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 14 " --> pdb=" O VAL A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 29 Processing helix chain 'A' and resid 31 through 42 removed outlier: 3.587A pdb=" N ARG A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 53 Processing helix chain 'A' and resid 76 through 92 removed outlier: 3.649A pdb=" N ALA A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 131 Processing helix chain 'A' and resid 132 through 140 Processing helix chain 'A' and resid 143 through 154 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.653A pdb=" N MET A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 402 removed outlier: 3.624A pdb=" N LEU A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 397 " --> pdb=" O PHE A 393 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 removed outlier: 3.607A pdb=" N LEU A 408 " --> pdb=" O PRO A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 430 Proline residue: A 421 - end of helix removed outlier: 3.875A pdb=" N LYS A 430 " --> pdb=" O CYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 454 removed outlier: 4.258A pdb=" N ASP A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) Proline residue: A 445 - end of helix removed outlier: 3.503A pdb=" N GLN A 454 " --> pdb=" O GLN A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 471 removed outlier: 3.837A pdb=" N ARG A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.781A pdb=" N TRP A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 474 through 479' Processing helix chain 'A' and resid 480 through 496 removed outlier: 3.624A pdb=" N GLU A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 530 through 558 removed outlier: 3.537A pdb=" N HIS A 534 " --> pdb=" O PRO A 530 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 544 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TRP A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET A 549 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 596 removed outlier: 3.960A pdb=" N LYS A 594 " --> pdb=" O ARG A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 611 removed outlier: 3.843A pdb=" N VAL A 606 " --> pdb=" O SER A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 672 removed outlier: 3.535A pdb=" N ARG A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 699 removed outlier: 3.858A pdb=" N ILE A 686 " --> pdb=" O GLY A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 737 removed outlier: 4.192A pdb=" N LEU A 725 " --> pdb=" O PRO A 721 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE A 732 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 733 " --> pdb=" O ILE A 729 " (cutoff:3.500A) Proline residue: A 735 - end of helix Processing helix chain 'A' and resid 772 through 783 Processing helix chain 'A' and resid 801 through 815 Processing helix chain 'A' and resid 835 through 854 removed outlier: 3.924A pdb=" N THR A 839 " --> pdb=" O SER A 835 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 844 " --> pdb=" O LEU A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 861 removed outlier: 4.650A pdb=" N ASP A 860 " --> pdb=" O GLY A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 889 removed outlier: 3.704A pdb=" N ALA A 880 " --> pdb=" O HIS A 876 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 887 " --> pdb=" O PHE A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 958 removed outlier: 3.848A pdb=" N SER A 957 " --> pdb=" O SER A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 982 removed outlier: 4.014A pdb=" N ARG A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 980 " --> pdb=" O GLY A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1018 removed outlier: 3.511A pdb=" N TYR A1010 " --> pdb=" O LEU A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1051 removed outlier: 4.418A pdb=" N ALA A1040 " --> pdb=" O ILE A1036 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1083 removed outlier: 4.046A pdb=" N VAL A1070 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN A1071 " --> pdb=" O SER A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1107 removed outlier: 4.052A pdb=" N GLY A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1119 removed outlier: 3.655A pdb=" N ALA A1114 " --> pdb=" O THR A1110 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 22 Processing helix chain 'K' and resid 27 through 37 Processing helix chain 'K' and resid 46 through 72 removed outlier: 3.730A pdb=" N TYR K 50 " --> pdb=" O GLY K 46 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE K 62 " --> pdb=" O LEU K 58 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU K 65 " --> pdb=" O GLU K 61 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN K 68 " --> pdb=" O GLU K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 90 removed outlier: 3.649A pdb=" N LEU K 83 " --> pdb=" O ILE K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 98 Processing helix chain 'L' and resid 37 through 49 removed outlier: 3.776A pdb=" N VAL L 44 " --> pdb=" O TYR L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 83 removed outlier: 3.725A pdb=" N ILE L 61 " --> pdb=" O LYS L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 102 removed outlier: 3.844A pdb=" N LEU L 100 " --> pdb=" O THR L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 124 removed outlier: 3.815A pdb=" N HIS L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 102 through 103 removed outlier: 3.542A pdb=" N VAL A 119 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 108 removed outlier: 3.981A pdb=" N ARG A 108 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLU A 113 " --> pdb=" O ARG A 108 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA5, first strand: chain 'A' and resid 561 through 564 removed outlier: 3.638A pdb=" N THR A 564 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 598 through 600 removed outlier: 4.313A pdb=" N GLN A 827 " --> pdb=" O HIS A 816 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N HIS A 816 " --> pdb=" O GLN A 827 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU A 617 " --> pdb=" O ALA A 817 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ARG A 819 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER A 619 " --> pdb=" O ARG A 819 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A 618 " --> pdb=" O ASP A 637 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 862 through 865 removed outlier: 3.542A pdb=" N VAL A 711 " --> pdb=" O PHE A 870 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 874 " --> pdb=" O TYR A 707 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR A 707 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP A 712 " --> pdb=" O VAL A 904 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 904 " --> pdb=" O ASP A 712 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 755 through 765 removed outlier: 3.999A pdb=" N ARG A 756 " --> pdb=" O LYS A 749 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 749 " --> pdb=" O ARG A 756 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 758 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N CYS A 740 " --> pdb=" O ASN A 799 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN A 799 " --> pdb=" O CYS A 740 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR A 744 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N SER A 795 " --> pdb=" O TYR A 744 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL A 746 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLU A 793 " --> pdb=" O VAL A 746 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N GLN A 748 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL A 791 " --> pdb=" O GLN A 748 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ALA A 750 " --> pdb=" O ALA A 789 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA A 789 " --> pdb=" O ALA A 750 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 928 through 929 Processing sheet with id=AB1, first strand: chain 'K' and resid 42 through 43 removed outlier: 6.581A pdb=" N ARG K 42 " --> pdb=" O ILE L 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 77 through 78 468 hydrogen bonds defined for protein. 1377 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 135 hydrogen bonds 266 hydrogen bond angles 0 basepair planarities 53 basepair parallelities 118 stacking parallelities Total time for adding SS restraints: 3.75 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3841 1.34 - 1.46: 4715 1.46 - 1.58: 6300 1.58 - 1.70: 494 1.70 - 1.82: 52 Bond restraints: 15402 Sorted by residual: bond pdb=" C PRO A 173 " pdb=" N PRO A 174 " ideal model delta sigma weight residual 1.332 1.364 -0.032 1.12e-02 7.97e+03 8.17e+00 bond pdb=" C1' DT S 20 " pdb=" N1 DT S 20 " ideal model delta sigma weight residual 1.468 1.501 -0.033 1.40e-02 5.10e+03 5.62e+00 bond pdb=" C ASN A1120 " pdb=" N PRO A1121 " ideal model delta sigma weight residual 1.332 1.352 -0.020 1.12e-02 7.97e+03 3.34e+00 bond pdb=" C1' DT S 19 " pdb=" N1 DT S 19 " ideal model delta sigma weight residual 1.468 1.492 -0.024 1.40e-02 5.10e+03 3.00e+00 bond pdb=" C3' DA S 21 " pdb=" C2' DA S 21 " ideal model delta sigma weight residual 1.516 1.530 -0.014 8.00e-03 1.56e+04 2.91e+00 ... (remaining 15397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 20849 1.41 - 2.82: 1003 2.82 - 4.23: 146 4.23 - 5.64: 51 5.64 - 7.05: 4 Bond angle restraints: 22053 Sorted by residual: angle pdb=" N3 DT S 19 " pdb=" C4 DT S 19 " pdb=" O4 DT S 19 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT S 20 " pdb=" C4 DT S 20 " pdb=" O4 DT S 20 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 angle pdb=" O4 DT S 19 " pdb=" C4 DT S 19 " pdb=" C5 DT S 19 " ideal model delta sigma weight residual 124.90 122.32 2.58 7.00e-01 2.04e+00 1.36e+01 angle pdb=" O4 DT S 20 " pdb=" C4 DT S 20 " pdb=" C5 DT S 20 " ideal model delta sigma weight residual 124.90 122.34 2.56 7.00e-01 2.04e+00 1.34e+01 angle pdb=" C3' C R 72 " pdb=" O3' C R 72 " pdb=" P G R 73 " ideal model delta sigma weight residual 119.70 123.75 -4.05 1.20e+00 6.94e-01 1.14e+01 ... (remaining 22048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 8277 35.43 - 70.86: 452 70.86 - 106.29: 22 106.29 - 141.72: 0 141.72 - 177.14: 4 Dihedral angle restraints: 8755 sinusoidal: 5353 harmonic: 3402 Sorted by residual: dihedral pdb=" C4' G R 326 " pdb=" C3' G R 326 " pdb=" C2' G R 326 " pdb=" C1' G R 326 " ideal model delta sinusoidal sigma weight residual 36.34 -36.00 72.35 1 3.10e+00 1.04e-01 6.96e+02 dihedral pdb=" C4' G R 308 " pdb=" C3' G R 308 " pdb=" C2' G R 308 " pdb=" C1' G R 308 " ideal model delta sinusoidal sigma weight residual 36.34 -35.85 72.19 1 3.10e+00 1.04e-01 6.93e+02 dihedral pdb=" C4' C R 243 " pdb=" C3' C R 243 " pdb=" C2' C R 243 " pdb=" C1' C R 243 " ideal model delta sinusoidal sigma weight residual 36.35 -35.77 72.11 1 3.10e+00 1.04e-01 6.92e+02 ... (remaining 8752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2289 0.066 - 0.132: 123 0.132 - 0.198: 3 0.198 - 0.264: 252 0.264 - 0.330: 21 Chirality restraints: 2688 Sorted by residual: chirality pdb=" P G R 73 " pdb=" OP1 G R 73 " pdb=" OP2 G R 73 " pdb=" O5' G R 73 " both_signs ideal model delta sigma weight residual True 2.17 -2.50 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" P C R 317 " pdb=" OP1 C R 317 " pdb=" OP2 C R 317 " pdb=" O5' C R 317 " both_signs ideal model delta sigma weight residual True 2.17 -2.47 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" P A R 126 " pdb=" OP1 A R 126 " pdb=" OP2 A R 126 " pdb=" O5' A R 126 " both_signs ideal model delta sigma weight residual True 2.17 -2.46 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 2685 not shown) Planarity restraints: 1895 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 68 " 0.040 5.00e-02 4.00e+02 6.14e-02 6.04e+00 pdb=" N PRO A 69 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 69 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 69 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE K 79 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO K 80 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO K 80 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO K 80 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A1043 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C CYS A1043 " -0.025 2.00e-02 2.50e+03 pdb=" O CYS A1043 " 0.009 2.00e-02 2.50e+03 pdb=" N TYR A1044 " 0.008 2.00e-02 2.50e+03 ... (remaining 1892 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3114 2.79 - 3.31: 12557 3.31 - 3.84: 24599 3.84 - 4.37: 27023 4.37 - 4.90: 42288 Nonbonded interactions: 109581 Sorted by model distance: nonbonded pdb=" O2' G R 76 " pdb=" OP1 U R 77 " model vdw 2.258 3.040 nonbonded pdb=" O2' C R 72 " pdb=" O5' G R 73 " model vdw 2.273 3.040 nonbonded pdb=" NH2 ARG A 390 " pdb=" OP2 C R 290 " model vdw 2.292 3.120 nonbonded pdb=" O ARG A 696 " pdb=" NE2 GLN A 700 " model vdw 2.314 3.120 nonbonded pdb=" OG SER A 619 " pdb=" O ALA A 817 " model vdw 2.324 3.040 ... (remaining 109576 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.810 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.070 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 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 0.035 15404 Z= 0.150 Angle : 0.725 7.050 22057 Z= 0.370 Chirality : 0.083 0.330 2688 Planarity : 0.004 0.061 1895 Dihedral : 17.346 177.144 6549 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.85 % Favored : 94.06 % Rotamer: Outliers : 0.10 % Allowed : 2.81 % Favored : 97.09 % 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: -3.21 (0.21), residues: 1162 helix: -1.05 (0.19), residues: 615 sheet: -1.52 (0.50), residues: 77 loop : -3.76 (0.22), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 979 TYR 0.007 0.001 TYR A 18 PHE 0.013 0.001 PHE A 776 TRP 0.005 0.001 TRP A 581 HIS 0.003 0.000 HIS A 815 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.15 (15402) covalent geometry : angle 0.72491 / 0.37 (22053) SS BOND : bond 0.01457 / 1.01 ( 2) SS BOND : angle 1.96310 / 1.12 ( 4) hydrogen bonds : bond 0.18735 / 12.33 ( 603) hydrogen bonds : angle 7.14241 / 5.23 ( 1643) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8189 (mt) cc_final: 0.7829 (mt) REVERT: A 378 ARG cc_start: 0.5594 (ttt180) cc_final: 0.3153 (mtt180) REVERT: A 452 LEU cc_start: 0.9325 (mt) cc_final: 0.8793 (pp) REVERT: K 73 ASN cc_start: 0.7407 (m110) cc_final: 0.7099 (p0) REVERT: K 82 HIS cc_start: 0.8773 (m-70) cc_final: 0.8518 (m90) REVERT: L 62 MET cc_start: 0.7049 (mmp) cc_final: 0.6450 (mtt) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.1965 time to fit residues: 46.1875 Evaluate side-chains 100 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.0470 chunk 10 optimal weight: 0.0970 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 GLN A 95 ASN A 402 GLN A 490 ASN A 506 GLN ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 HIS A 906 ASN A 921 GLN A1022 HIS A1023 GLN K 31 HIS ** K 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.116604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.089198 restraints weight = 86024.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.091081 restraints weight = 45815.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.092574 restraints weight = 33503.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.093124 restraints weight = 28326.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.093124 restraints weight = 26553.413| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 15404 Z= 0.175 Angle : 1.041 22.979 22057 Z= 0.419 Chirality : 0.084 1.063 2688 Planarity : 0.005 0.050 1895 Dihedral : 15.904 173.581 4290 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.37 % Favored : 93.55 % Rotamer: Outliers : 1.81 % Allowed : 11.63 % 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: -1.88 (0.23), residues: 1162 helix: 0.16 (0.21), residues: 615 sheet: -0.89 (0.52), residues: 76 loop : -3.34 (0.23), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 811 TYR 0.018 0.002 TYR A 325 PHE 0.021 0.002 PHE A 708 TRP 0.010 0.001 TRP A 519 HIS 0.004 0.001 HIS A 752 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (15402) covalent geometry : angle 1.04071 / 0.42 (22053) SS BOND : bond 0.00302 / 0.20 ( 2) SS BOND : angle 1.06357 / 0.60 ( 4) hydrogen bonds : bond 0.05635 / 3.52 ( 603) hydrogen bonds : angle 4.25286 / 3.03 ( 1643) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6433 (pm20) REVERT: A 332 LEU cc_start: 0.8225 (mt) cc_final: 0.7956 (mt) REVERT: A 378 ARG cc_start: 0.5648 (ttt180) cc_final: 0.3154 (mtt180) REVERT: A 452 LEU cc_start: 0.9303 (mt) cc_final: 0.8854 (pp) REVERT: A 872 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8313 (mt) REVERT: A 979 ARG cc_start: 0.8047 (ttm-80) cc_final: 0.7753 (ttm110) outliers start: 18 outliers final: 6 residues processed: 118 average time/residue: 0.1526 time to fit residues: 25.1349 Evaluate side-chains 90 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain L residue 45 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 87 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 121 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 6 optimal weight: 40.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 HIS A 490 ASN A 534 HIS ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 HIS ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 GLN A 876 HIS A1102 GLN ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.105832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.076300 restraints weight = 85985.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.078227 restraints weight = 46248.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.079322 restraints weight = 33814.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.079707 restraints weight = 29324.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.080131 restraints weight = 27702.600| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 15404 Z= 0.303 Angle : 1.046 13.510 22057 Z= 0.452 Chirality : 0.067 0.435 2688 Planarity : 0.007 0.071 1895 Dihedral : 16.401 168.764 4290 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.37 % Favored : 93.55 % Rotamer: Outliers : 3.41 % Allowed : 15.55 % Favored : 81.04 % 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 (0.23), residues: 1162 helix: 0.39 (0.20), residues: 625 sheet: -0.90 (0.47), residues: 97 loop : -3.31 (0.24), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 486 TYR 0.027 0.003 TYR A 638 PHE 0.028 0.004 PHE A 487 TRP 0.017 0.002 TRP A 387 HIS 0.051 0.004 HIS K 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.30 (15402) covalent geometry : angle 1.04541 / 0.45 (22053) SS BOND : bond 0.06785 / 4.84 ( 2) SS BOND : angle 3.25086 / 2.84 ( 4) hydrogen bonds : bond 0.06931 / 4.64 ( 603) hydrogen bonds : angle 4.44762 / 3.17 ( 1643) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 89 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8376 (mt) cc_final: 0.8071 (mt) REVERT: A 389 MET cc_start: 0.8057 (mtm) cc_final: 0.7807 (mtm) REVERT: A 1059 LYS cc_start: 0.8285 (mmtm) cc_final: 0.8024 (tptt) outliers start: 34 outliers final: 22 residues processed: 111 average time/residue: 0.1477 time to fit residues: 23.1665 Evaluate side-chains 96 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 500 HIS Chi-restraints excluded: chain A residue 662 PHE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 121 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 7 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 HIS L 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.107064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.077655 restraints weight = 85611.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.079705 restraints weight = 45455.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.080781 restraints weight = 33720.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.081190 restraints weight = 29411.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.081814 restraints weight = 27729.525| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 15404 Z= 0.154 Angle : 0.835 13.118 22057 Z= 0.349 Chirality : 0.060 0.426 2688 Planarity : 0.004 0.052 1895 Dihedral : 15.911 165.710 4290 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.11 % Favored : 93.80 % Rotamer: Outliers : 2.51 % Allowed : 17.65 % Favored : 79.84 % 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: -1.09 (0.24), residues: 1162 helix: 0.84 (0.21), residues: 628 sheet: -0.66 (0.51), residues: 92 loop : -3.19 (0.25), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 390 TYR 0.021 0.002 TYR A 638 PHE 0.020 0.002 PHE A 883 TRP 0.016 0.001 TRP A 510 HIS 0.008 0.001 HIS K 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (15402) covalent geometry : angle 0.83459 / 0.35 (22053) SS BOND : bond 0.02586 / 1.84 ( 2) SS BOND : angle 1.68586 / 1.32 ( 4) hydrogen bonds : bond 0.05112 / 3.34 ( 603) hydrogen bonds : angle 4.03980 / 2.86 ( 1643) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8412 (mt) cc_final: 0.8096 (mt) REVERT: A 389 MET cc_start: 0.7982 (mtm) cc_final: 0.7739 (mtm) REVERT: A 452 LEU cc_start: 0.9349 (mt) cc_final: 0.8795 (pp) REVERT: A 774 ARG cc_start: 0.8474 (ttt180) cc_final: 0.8251 (tmm160) REVERT: A 779 HIS cc_start: 0.8818 (OUTLIER) cc_final: 0.8597 (t70) outliers start: 25 outliers final: 14 residues processed: 95 average time/residue: 0.1443 time to fit residues: 19.6126 Evaluate side-chains 89 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 500 HIS Chi-restraints excluded: chain A residue 662 PHE Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 744 TYR Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 121 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 39 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 62 optimal weight: 9.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 GLN ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 HIS ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 GLN L 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.104982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.076536 restraints weight = 84415.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.077881 restraints weight = 45959.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.078814 restraints weight = 33217.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.079164 restraints weight = 28740.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.079164 restraints weight = 26949.034| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15404 Z= 0.172 Angle : 0.827 12.670 22057 Z= 0.346 Chirality : 0.059 0.404 2688 Planarity : 0.004 0.055 1895 Dihedral : 15.838 164.677 4290 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.54 % Favored : 93.37 % Rotamer: Outliers : 3.31 % Allowed : 18.56 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.84 (0.25), residues: 1162 helix: 1.06 (0.21), residues: 628 sheet: -0.57 (0.52), residues: 92 loop : -3.09 (0.25), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 470 TYR 0.020 0.002 TYR A 638 PHE 0.020 0.002 PHE A 776 TRP 0.013 0.001 TRP A 510 HIS 0.005 0.001 HIS A 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (15402) covalent geometry : angle 0.82676 / 0.35 (22053) SS BOND : bond 0.01236 / 0.86 ( 2) SS BOND : angle 1.79496 / 1.49 ( 4) hydrogen bonds : bond 0.04977 / 3.28 ( 603) hydrogen bonds : angle 3.99150 / 2.84 ( 1643) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 78 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8445 (mt) cc_final: 0.8193 (mt) REVERT: A 389 MET cc_start: 0.7979 (mtm) cc_final: 0.7650 (mtm) REVERT: A 922 MET cc_start: 0.7124 (pmm) cc_final: 0.6903 (ptt) outliers start: 33 outliers final: 24 residues processed: 101 average time/residue: 0.1196 time to fit residues: 18.2473 Evaluate side-chains 96 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 500 HIS Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 744 TYR Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 121 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 81 optimal weight: 0.4980 chunk 117 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.105049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.076224 restraints weight = 84232.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.077786 restraints weight = 45337.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.078716 restraints weight = 32436.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.079053 restraints weight = 28082.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.079053 restraints weight = 26618.628| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15404 Z= 0.145 Angle : 0.797 12.159 22057 Z= 0.333 Chirality : 0.058 0.408 2688 Planarity : 0.004 0.055 1895 Dihedral : 15.696 166.384 4290 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.20 % Favored : 93.72 % Rotamer: Outliers : 3.21 % Allowed : 19.26 % Favored : 77.53 % 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: -0.76 (0.25), residues: 1162 helix: 1.09 (0.21), residues: 636 sheet: -0.51 (0.52), residues: 92 loop : -3.09 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 774 TYR 0.016 0.002 TYR A 638 PHE 0.013 0.001 PHE A 776 TRP 0.011 0.001 TRP A 510 HIS 0.006 0.001 HIS A 779 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (15402) covalent geometry : angle 0.79634 / 0.33 (22053) SS BOND : bond 0.01787 / 1.26 ( 2) SS BOND : angle 2.18443 / 1.77 ( 4) hydrogen bonds : bond 0.04688 / 3.08 ( 603) hydrogen bonds : angle 3.94445 / 2.79 ( 1643) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 74 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7611 (pm20) REVERT: A 332 LEU cc_start: 0.8485 (mt) cc_final: 0.8215 (mt) REVERT: A 389 MET cc_start: 0.7931 (mtm) cc_final: 0.7626 (mtm) REVERT: A 690 TRP cc_start: 0.8502 (OUTLIER) cc_final: 0.8270 (t60) outliers start: 32 outliers final: 20 residues processed: 96 average time/residue: 0.1200 time to fit residues: 17.4873 Evaluate side-chains 93 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 500 HIS Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 690 TRP Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 744 TYR Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1025 VAL Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 121 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 28 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 34 optimal weight: 0.5980 chunk 88 optimal weight: 0.3980 chunk 75 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 99 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 HIS L 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.104656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.075510 restraints weight = 84144.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.077441 restraints weight = 44400.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.078519 restraints weight = 32272.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.078723 restraints weight = 27911.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.078723 restraints weight = 26493.553| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15404 Z= 0.138 Angle : 0.781 12.884 22057 Z= 0.326 Chirality : 0.058 0.413 2688 Planarity : 0.004 0.056 1895 Dihedral : 15.603 165.477 4290 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.02 % Favored : 93.89 % Rotamer: Outliers : 3.31 % Allowed : 19.36 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.25), residues: 1162 helix: 1.22 (0.22), residues: 632 sheet: -0.49 (0.53), residues: 92 loop : -2.98 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 774 TYR 0.016 0.002 TYR A 638 PHE 0.015 0.001 PHE A 776 TRP 0.010 0.001 TRP A 510 HIS 0.005 0.001 HIS A 779 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (15402) covalent geometry : angle 0.78003 / 0.33 (22053) SS BOND : bond 0.01375 / 0.96 ( 2) SS BOND : angle 2.23521 / 1.49 ( 4) hydrogen bonds : bond 0.04483 / 2.94 ( 603) hydrogen bonds : angle 3.88757 / 2.75 ( 1643) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 75 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7872 (pm20) REVERT: A 332 LEU cc_start: 0.8464 (mt) cc_final: 0.8235 (mt) REVERT: A 389 MET cc_start: 0.7959 (mtm) cc_final: 0.7576 (mtm) REVERT: A 657 ARG cc_start: 0.8786 (mtp180) cc_final: 0.8574 (ptp-110) REVERT: A 690 TRP cc_start: 0.8523 (OUTLIER) cc_final: 0.8211 (t60) REVERT: A 729 ILE cc_start: 0.9173 (mm) cc_final: 0.8890 (mt) outliers start: 33 outliers final: 24 residues processed: 99 average time/residue: 0.1270 time to fit residues: 18.8242 Evaluate side-chains 100 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 500 HIS Chi-restraints excluded: chain A residue 662 PHE Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 690 TRP Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 744 TYR Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 121 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 87 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 32 optimal weight: 0.0980 chunk 30 optimal weight: 0.9980 chunk 113 optimal weight: 0.0070 chunk 126 optimal weight: 6.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.105400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.076081 restraints weight = 84846.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.078105 restraints weight = 45448.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.079202 restraints weight = 33149.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.079605 restraints weight = 28613.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.079605 restraints weight = 27076.968| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15404 Z= 0.120 Angle : 0.780 13.031 22057 Z= 0.324 Chirality : 0.057 0.428 2688 Planarity : 0.004 0.054 1895 Dihedral : 15.522 165.540 4290 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.94 % Favored : 93.98 % Rotamer: Outliers : 2.11 % Allowed : 20.96 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.25), residues: 1162 helix: 1.25 (0.22), residues: 633 sheet: -0.41 (0.52), residues: 92 loop : -2.94 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 774 TYR 0.013 0.001 TYR A 638 PHE 0.011 0.001 PHE A 159 TRP 0.010 0.001 TRP A 510 HIS 0.005 0.001 HIS K 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (15402) covalent geometry : angle 0.77951 / 0.32 (22053) SS BOND : bond 0.00997 / 0.70 ( 2) SS BOND : angle 1.96074 / 1.10 ( 4) hydrogen bonds : bond 0.04327 / 2.83 ( 603) hydrogen bonds : angle 3.82692 / 2.70 ( 1643) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7884 (pm20) REVERT: A 332 LEU cc_start: 0.8474 (mt) cc_final: 0.8258 (mt) REVERT: A 389 MET cc_start: 0.7964 (mtm) cc_final: 0.7648 (mtm) REVERT: A 452 LEU cc_start: 0.9347 (mt) cc_final: 0.8755 (pp) REVERT: A 657 ARG cc_start: 0.8798 (mtp180) cc_final: 0.8589 (ptp-110) REVERT: A 729 ILE cc_start: 0.9158 (mm) cc_final: 0.8874 (mt) outliers start: 21 outliers final: 17 residues processed: 94 average time/residue: 0.1261 time to fit residues: 17.8021 Evaluate side-chains 89 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 744 TYR Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 1025 VAL Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 121 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 116 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.104969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.076470 restraints weight = 84809.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.077681 restraints weight = 47341.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.078159 restraints weight = 33804.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.079070 restraints weight = 29841.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.079070 restraints weight = 27454.572| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15404 Z= 0.128 Angle : 0.775 13.336 22057 Z= 0.324 Chirality : 0.057 0.445 2688 Planarity : 0.004 0.051 1895 Dihedral : 15.482 167.452 4290 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.77 % Favored : 94.15 % Rotamer: Outliers : 2.31 % Allowed : 21.26 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.26), residues: 1162 helix: 1.29 (0.22), residues: 633 sheet: -0.30 (0.53), residues: 92 loop : -2.85 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 811 TYR 0.013 0.001 TYR A 638 PHE 0.020 0.001 PHE A 812 TRP 0.008 0.001 TRP A 510 HIS 0.011 0.001 HIS A 779 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (15402) covalent geometry : angle 0.77446 / 0.32 (22053) SS BOND : bond 0.01495 / 1.06 ( 2) SS BOND : angle 2.04990 / 1.16 ( 4) hydrogen bonds : bond 0.04376 / 2.88 ( 603) hydrogen bonds : angle 3.86489 / 2.72 ( 1643) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8437 (mt) cc_final: 0.8209 (mt) REVERT: A 389 MET cc_start: 0.7998 (mtm) cc_final: 0.7675 (mtm) REVERT: A 690 TRP cc_start: 0.8559 (OUTLIER) cc_final: 0.8255 (t60) REVERT: A 729 ILE cc_start: 0.9138 (mm) cc_final: 0.8855 (mt) outliers start: 23 outliers final: 18 residues processed: 90 average time/residue: 0.1177 time to fit residues: 15.9794 Evaluate side-chains 88 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 690 TRP Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 744 TYR Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1025 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 121 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 22 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 33 optimal weight: 0.0770 chunk 13 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.104054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.074739 restraints weight = 84227.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.076519 restraints weight = 45602.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.077181 restraints weight = 33944.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.078149 restraints weight = 30329.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.078337 restraints weight = 27897.315| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15404 Z= 0.142 Angle : 0.789 13.910 22057 Z= 0.329 Chirality : 0.057 0.465 2688 Planarity : 0.004 0.052 1895 Dihedral : 15.468 170.901 4290 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.94 % Favored : 93.98 % Rotamer: Outliers : 2.21 % Allowed : 21.56 % Favored : 76.23 % 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: -0.47 (0.26), residues: 1162 helix: 1.28 (0.22), residues: 634 sheet: -0.35 (0.54), residues: 92 loop : -2.84 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 653 TYR 0.013 0.001 TYR A 638 PHE 0.018 0.002 PHE A 776 TRP 0.008 0.001 TRP A 547 HIS 0.010 0.001 HIS A 779 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (15402) covalent geometry : angle 0.78848 / 0.33 (22053) SS BOND : bond 0.01533 / 1.08 ( 2) SS BOND : angle 1.91685 / 1.15 ( 4) hydrogen bonds : bond 0.04514 / 3.00 ( 603) hydrogen bonds : angle 3.86005 / 2.72 ( 1643) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8374 (mt) cc_final: 0.8160 (mt) REVERT: A 389 MET cc_start: 0.8005 (mtm) cc_final: 0.7660 (mtm) REVERT: A 690 TRP cc_start: 0.8601 (OUTLIER) cc_final: 0.8199 (t60) REVERT: A 729 ILE cc_start: 0.9134 (mm) cc_final: 0.8852 (mt) REVERT: A 922 MET cc_start: 0.7328 (pmm) cc_final: 0.7089 (ptt) REVERT: L 54 ILE cc_start: 0.7563 (pt) cc_final: 0.7337 (mm) outliers start: 22 outliers final: 20 residues processed: 85 average time/residue: 0.1292 time to fit residues: 16.5123 Evaluate side-chains 88 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 690 TRP Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 744 TYR Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1025 VAL Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 121 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 75 optimal weight: 0.0070 chunk 19 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.104716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.076326 restraints weight = 83750.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.077719 restraints weight = 45510.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.078605 restraints weight = 33220.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.079163 restraints weight = 28773.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.079330 restraints weight = 26882.242| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.5667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15404 Z= 0.118 Angle : 0.769 13.403 22057 Z= 0.319 Chirality : 0.056 0.434 2688 Planarity : 0.004 0.052 1895 Dihedral : 15.386 174.514 4290 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.59 % Favored : 94.32 % Rotamer: Outliers : 2.01 % Allowed : 21.87 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.41 (0.26), residues: 1162 helix: 1.37 (0.22), residues: 632 sheet: -0.41 (0.55), residues: 86 loop : -2.83 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 378 TYR 0.012 0.001 TYR A 638 PHE 0.021 0.001 PHE A 812 TRP 0.009 0.001 TRP A 510 HIS 0.009 0.001 HIS A 779 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (15402) covalent geometry : angle 0.76835 / 0.32 (22053) SS BOND : bond 0.01464 / 1.03 ( 2) SS BOND : angle 1.79299 / 1.07 ( 4) hydrogen bonds : bond 0.04248 / 2.80 ( 603) hydrogen bonds : angle 3.82940 / 2.69 ( 1643) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4152.44 seconds wall clock time: 71 minutes 46.84 seconds (4306.84 seconds total)