Starting phenix.real_space_refine on Fri Jul 3 15:19:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v99_31811/07_2026/7v99_31811.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v99_31811/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7v99_31811/07_2026/7v99_31811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v99_31811/07_2026/7v99_31811.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7v99_31811/07_2026/7v99_31811.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v99_31811/07_2026/7v99_31811.cif" model { file = "/net/cci-nas-00/data/ceres_data/7v99_31811/07_2026/7v99_31811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v99_31811/07_2026/7v99_31811.cif" } 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-dev-6108/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: {'RNA': 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: 2.66, per 1000 atoms: 0.18 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: 0.96 Conformation dependent library (CDL) restraints added in 365.7 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: 1.50 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: 3.43 Time building geometry restraints manager: 1.33 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: 21443 1.41 - 2.82: 514 2.82 - 4.23: 66 4.23 - 5.64: 26 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=" N GLN A 569 " pdb=" CA GLN A 569 " pdb=" C GLN A 569 " ideal model delta sigma weight residual 110.44 106.41 4.03 1.20e+00 6.94e-01 1.13e+01 ... (remaining 22048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 8533 35.43 - 70.86: 199 70.86 - 106.29: 18 106.29 - 141.72: 1 141.72 - 177.14: 4 Dihedral angle restraints: 8755 sinusoidal: 5353 harmonic: 3402 Sorted by residual: dihedral pdb=" CB CYS A 982 " pdb=" SG CYS A 982 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 45.52 47.48 1 1.00e+01 1.00e-02 3.11e+01 dihedral pdb=" CA GLN A 569 " pdb=" C GLN A 569 " pdb=" N LYS A 570 " pdb=" CA LYS A 570 " ideal model delta harmonic sigma weight residual -180.00 -156.12 -23.88 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" C4' G R 76 " pdb=" C3' G R 76 " pdb=" O3' G R 76 " pdb=" P U R 77 " ideal model delta sinusoidal sigma weight residual -140.00 37.14 -177.14 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 8752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2093 0.028 - 0.057: 419 0.057 - 0.085: 113 0.085 - 0.113: 51 0.113 - 0.142: 12 Chirality restraints: 2688 Sorted by residual: chirality pdb=" C3' C R 72 " pdb=" C4' C R 72 " pdb=" O3' C R 72 " pdb=" C2' C R 72 " both_signs ideal model delta sigma weight residual False -2.48 -2.34 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" C1' A R 174 " pdb=" O4' A R 174 " pdb=" C2' A R 174 " pdb=" N9 A R 174 " both_signs ideal model delta sigma weight residual False 2.46 2.32 0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CB THR A 375 " pdb=" CA THR A 375 " pdb=" OG1 THR A 375 " pdb=" CG2 THR A 375 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.14 2.00e-01 2.50e+01 4.61e-01 ... (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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.840 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.580 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.940 ------------------------------------------------------------------------------- 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 : 0.002 0.035 15404 Z= 0.137 Angle : 0.535 7.050 22057 Z= 0.329 Chirality : 0.029 0.142 2688 Planarity : 0.004 0.061 1895 Dihedral : 14.530 177.144 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 0.00215 / 0.14 (15402) covalent geometry : angle 0.53424 / 0.33 (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 : 0.346 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: 0.1878 time to fit residues: 44.1530 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 : 0.436 ------------------------------------------------------------------------------- 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: 0.6980 chunk 10 optimal weight: 0.0970 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 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: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 GLN A 95 ASN A 402 GLN A 490 ASN ** A 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4581 r_free = 0.4581 target = 0.116317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.091352 restraints weight = 86549.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.093754 restraints weight = 47606.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.095064 restraints weight = 31255.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.094497 restraints weight = 29938.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.094042 restraints weight = 26782.740| |-----------------------------------------------------------------------------| r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15404 Z= 0.133 Angle : 0.581 8.454 22057 Z= 0.280 Chirality : 0.033 0.218 2688 Planarity : 0.005 0.050 1895 Dihedral : 13.021 170.714 4290 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.20 % Favored : 93.72 % 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: -1.92 (0.23), residues: 1162 helix: 0.13 (0.21), residues: 615 sheet: -0.93 (0.51), residues: 76 loop : -3.35 (0.23), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 81 TYR 0.019 0.002 TYR A 667 PHE 0.018 0.002 PHE A 708 TRP 0.010 0.001 TRP A 519 HIS 0.004 0.001 HIS A 925 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (15402) covalent geometry : angle 0.58060 / 0.28 (22053) SS BOND : bond 0.00787 / 0.56 ( 2) SS BOND : angle 1.43190 / 0.86 ( 4) hydrogen bonds : bond 0.05921 / 3.72 ( 603) hydrogen bonds : angle 4.29428 / 3.05 ( 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 121 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.439 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: 0.7000 (OUTLIER) cc_final: 0.6484 (pm20) REVERT: A 332 LEU cc_start: 0.8264 (mt) cc_final: 0.7985 (mt) REVERT: A 378 ARG cc_start: 0.5628 (ttt180) cc_final: 0.3159 (mtt180) REVERT: A 452 LEU cc_start: 0.9305 (mt) cc_final: 0.8856 (pp) outliers start: 18 outliers final: 7 residues processed: 115 average time/residue: 0.1448 time to fit residues: 23.2696 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 : 0.366 ------------------------------------------------------------------------------- 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: 0.3980 chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 HIS A 490 ASN ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 GLN ** K 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.110673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.084771 restraints weight = 85056.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.086429 restraints weight = 47445.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.086352 restraints weight = 33050.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.086279 restraints weight = 31270.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.086312 restraints weight = 28913.747| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 15404 Z= 0.190 Angle : 0.624 10.464 22057 Z= 0.312 Chirality : 0.036 0.293 2688 Planarity : 0.005 0.051 1895 Dihedral : 13.116 169.101 4290 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.54 % Favored : 93.37 % Rotamer: Outliers : 2.11 % Allowed : 15.25 % Favored : 82.65 % 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: -1.26 (0.24), residues: 1162 helix: 0.71 (0.21), residues: 623 sheet: -0.79 (0.52), residues: 78 loop : -3.16 (0.24), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 486 TYR 0.019 0.002 TYR A 638 PHE 0.019 0.002 PHE A 487 TRP 0.010 0.001 TRP A 510 HIS 0.026 0.002 HIS K 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (15402) covalent geometry : angle 0.62343 / 0.31 (22053) SS BOND : bond 0.02126 / 1.51 ( 2) SS BOND : angle 1.53697 / 1.14 ( 4) hydrogen bonds : bond 0.05527 / 3.60 ( 603) hydrogen bonds : angle 4.14558 / 2.96 ( 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 109 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.434 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: 0.8357 (mt) cc_final: 0.8004 (mt) REVERT: A 378 ARG cc_start: 0.5821 (ttt180) cc_final: 0.3315 (mtt180) REVERT: A 452 LEU cc_start: 0.9331 (mt) cc_final: 0.8822 (pp) REVERT: A 773 MET cc_start: 0.8791 (mpp) cc_final: 0.8467 (mpp) outliers start: 21 outliers final: 16 residues processed: 102 average time/residue: 0.1355 time to fit residues: 19.7668 Evaluate side-chains 94 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 500 HIS Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain K residue 31 HIS 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: 4.9990 chunk 137 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 83 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 134 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 GLN ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.107225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.080063 restraints weight = 85615.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.081939 restraints weight = 48280.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.083246 restraints weight = 33501.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.082170 restraints weight = 31178.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.081729 restraints weight = 29685.388| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 15404 Z= 0.176 Angle : 0.613 11.487 22057 Z= 0.309 Chirality : 0.036 0.197 2688 Planarity : 0.005 0.054 1895 Dihedral : 13.317 169.599 4290 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.45 % Favored : 93.46 % Rotamer: Outliers : 3.41 % Allowed : 16.35 % Favored : 80.24 % 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: -1.02 (0.25), residues: 1162 helix: 0.92 (0.21), residues: 632 sheet: -0.68 (0.51), residues: 92 loop : -3.20 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 979 TYR 0.022 0.002 TYR A 638 PHE 0.019 0.002 PHE A1031 TRP 0.011 0.001 TRP A 510 HIS 0.024 0.002 HIS K 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 (15402) covalent geometry : angle 0.61197 / 0.31 (22053) SS BOND : bond 0.01276 / 0.90 ( 2) SS BOND : angle 2.20900 / 1.83 ( 4) hydrogen bonds : bond 0.05192 / 3.41 ( 603) hydrogen bonds : angle 4.04448 / 2.88 ( 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 117 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 83 time to evaluate : 0.347 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 324 VAL cc_start: 0.7055 (OUTLIER) cc_final: 0.6789 (m) REVERT: A 332 LEU cc_start: 0.8318 (mt) cc_final: 0.7967 (mt) REVERT: A 452 LEU cc_start: 0.9342 (mt) cc_final: 0.8806 (pp) outliers start: 34 outliers final: 17 residues processed: 108 average time/residue: 0.1218 time to fit residues: 18.9382 Evaluate side-chains 94 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 420 THR Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 500 HIS Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 706 LEU 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 862 LEU Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1111 THR 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: 0.0270 chunk 2 optimal weight: 0.6980 chunk 134 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 GLN K 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.107925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.078362 restraints weight = 85268.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.080352 restraints weight = 45684.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.080826 restraints weight = 34013.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.081291 restraints weight = 30403.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.081291 restraints weight = 29057.673| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15404 Z= 0.118 Angle : 0.556 11.905 22057 Z= 0.274 Chirality : 0.035 0.363 2688 Planarity : 0.004 0.053 1895 Dihedral : 13.223 169.352 4290 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.63 % Favored : 93.29 % Rotamer: Outliers : 2.51 % Allowed : 18.76 % Favored : 78.74 % 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: -0.73 (0.25), residues: 1162 helix: 1.13 (0.22), residues: 628 sheet: -0.39 (0.56), residues: 78 loop : -2.98 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 486 TYR 0.017 0.002 TYR A 638 PHE 0.018 0.001 PHE A 776 TRP 0.014 0.001 TRP A 510 HIS 0.006 0.001 HIS A 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (15402) covalent geometry : angle 0.55600 / 0.27 (22053) SS BOND : bond 0.00622 / 0.41 ( 2) SS BOND : angle 1.39804 / 1.15 ( 4) hydrogen bonds : bond 0.04591 / 2.98 ( 603) hydrogen bonds : angle 3.89098 / 2.77 ( 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 104 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.466 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 324 VAL cc_start: 0.7075 (t) cc_final: 0.6784 (m) REVERT: A 327 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7237 (pm20) REVERT: A 332 LEU cc_start: 0.8303 (mt) cc_final: 0.7937 (mt) REVERT: A 378 ARG cc_start: 0.5823 (ttt180) cc_final: 0.3507 (mtt180) REVERT: A 452 LEU cc_start: 0.9340 (mt) cc_final: 0.8857 (pp) REVERT: A 922 MET cc_start: 0.6822 (pmm) cc_final: 0.6551 (ptt) outliers start: 25 outliers final: 15 residues processed: 97 average time/residue: 0.1253 time to fit residues: 17.7760 Evaluate side-chains 91 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 360 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 500 HIS 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 844 LEU Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 877 LEU 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: 10.0000 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 81 optimal weight: 0.6980 chunk 117 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 18 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.107217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.078239 restraints weight = 85133.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.079811 restraints weight = 46345.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.080723 restraints weight = 33530.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.080866 restraints weight = 29420.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.080866 restraints weight = 27857.918| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 15404 Z= 0.119 Angle : 0.551 12.510 22057 Z= 0.271 Chirality : 0.033 0.192 2688 Planarity : 0.004 0.055 1895 Dihedral : 13.166 170.497 4290 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.28 % Favored : 93.63 % Rotamer: Outliers : 3.41 % Allowed : 18.76 % Favored : 77.83 % 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: -0.59 (0.25), residues: 1162 helix: 1.25 (0.22), residues: 627 sheet: -0.32 (0.57), residues: 78 loop : -2.90 (0.25), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 979 TYR 0.015 0.001 TYR A 638 PHE 0.014 0.001 PHE A 776 TRP 0.010 0.001 TRP A 510 HIS 0.003 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (15402) covalent geometry : angle 0.55076 / 0.27 (22053) SS BOND : bond 0.02774 / 1.98 ( 2) SS BOND : angle 1.49601 / 0.84 ( 4) hydrogen bonds : bond 0.04393 / 2.87 ( 603) hydrogen bonds : angle 3.83699 / 2.72 ( 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 113 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.397 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 324 VAL cc_start: 0.7135 (t) cc_final: 0.6805 (m) REVERT: A 327 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7340 (pm20) REVERT: A 332 LEU cc_start: 0.8262 (mt) cc_final: 0.7906 (mt) REVERT: A 378 ARG cc_start: 0.5978 (ttt180) cc_final: 0.3747 (mtt180) REVERT: A 452 LEU cc_start: 0.9346 (mt) cc_final: 0.8818 (pp) REVERT: A 922 MET cc_start: 0.6997 (pmm) cc_final: 0.6738 (ptt) outliers start: 34 outliers final: 23 residues processed: 103 average time/residue: 0.1123 time to fit residues: 17.1725 Evaluate side-chains 98 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 500 HIS 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 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 862 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain K residue 31 HIS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 28 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 34 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 7 optimal weight: 0.4980 chunk 99 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 135 optimal weight: 8.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 GLN A 815 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.106246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.076799 restraints weight = 84701.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.078756 restraints weight = 45619.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.079247 restraints weight = 33045.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.080438 restraints weight = 29379.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.080653 restraints weight = 26688.436| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.4464 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= 0.125 Angle : 0.565 13.060 22057 Z= 0.275 Chirality : 0.034 0.425 2688 Planarity : 0.004 0.056 1895 Dihedral : 13.171 170.531 4290 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.11 % Favored : 93.80 % Rotamer: Outliers : 3.21 % Allowed : 19.36 % Favored : 77.43 % 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: -0.58 (0.25), residues: 1162 helix: 1.22 (0.22), residues: 635 sheet: -0.34 (0.57), residues: 78 loop : -2.90 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 774 TYR 0.017 0.002 TYR A 717 PHE 0.025 0.001 PHE A 776 TRP 0.008 0.001 TRP A 510 HIS 0.005 0.001 HIS A 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (15402) covalent geometry : angle 0.56454 / 0.28 (22053) SS BOND : bond 0.01872 / 1.31 ( 2) SS BOND : angle 2.00846 / 1.54 ( 4) hydrogen bonds : bond 0.04389 / 2.90 ( 603) hydrogen bonds : angle 3.81257 / 2.71 ( 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 109 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 77 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 VAL cc_start: 0.7006 (t) cc_final: 0.6611 (m) REVERT: A 327 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7419 (pm20) REVERT: A 332 LEU cc_start: 0.8252 (mt) cc_final: 0.7889 (mt) REVERT: A 774 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7493 (tmm160) outliers start: 32 outliers final: 22 residues processed: 100 average time/residue: 0.1155 time to fit residues: 17.3140 Evaluate side-chains 98 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 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 681 LEU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 774 ARG Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain L residue 45 LEU 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: 0.9980 chunk 122 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 chunk 13 optimal weight: 50.0000 chunk 109 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 GLN ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.106228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.076871 restraints weight = 84393.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.078600 restraints weight = 45250.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.079761 restraints weight = 33675.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.080183 restraints weight = 28963.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.080183 restraints weight = 27349.161| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.4588 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= 0.117 Angle : 0.550 13.153 22057 Z= 0.269 Chirality : 0.034 0.339 2688 Planarity : 0.005 0.104 1895 Dihedral : 13.155 170.608 4290 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.02 % Favored : 93.89 % Rotamer: Outliers : 3.11 % Allowed : 19.96 % 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: -0.51 (0.25), residues: 1162 helix: 1.28 (0.22), residues: 633 sheet: -0.27 (0.57), residues: 78 loop : -2.87 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 91 TYR 0.014 0.001 TYR A 717 PHE 0.017 0.001 PHE A 776 TRP 0.008 0.001 TRP A 510 HIS 0.004 0.001 HIS K 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (15402) covalent geometry : angle 0.54962 / 0.27 (22053) SS BOND : bond 0.01345 / 0.95 ( 2) SS BOND : angle 1.88313 / 1.38 ( 4) hydrogen bonds : bond 0.04267 / 2.81 ( 603) hydrogen bonds : angle 3.81028 / 2.71 ( 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 105 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 VAL cc_start: 0.6984 (t) cc_final: 0.6613 (m) REVERT: A 327 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7461 (pm20) REVERT: A 332 LEU cc_start: 0.8255 (mt) cc_final: 0.7873 (mt) REVERT: A 452 LEU cc_start: 0.9309 (mt) cc_final: 0.8727 (pp) outliers start: 31 outliers final: 27 residues processed: 96 average time/residue: 0.1132 time to fit residues: 16.5332 Evaluate side-chains 101 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 327 GLU 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 664 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 706 LEU 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 794 GLN Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain K residue 31 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 116 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 85 optimal weight: 0.2980 chunk 21 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 6 optimal weight: 0.3980 chunk 33 optimal weight: 0.0070 overall best weight: 0.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.106667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.077240 restraints weight = 84440.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.079232 restraints weight = 45085.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.080421 restraints weight = 33137.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.080707 restraints weight = 28486.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.080708 restraints weight = 26979.165| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 15404 Z= 0.102 Angle : 0.549 13.333 22057 Z= 0.266 Chirality : 0.033 0.324 2688 Planarity : 0.004 0.084 1895 Dihedral : 13.115 170.612 4290 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.20 % Favored : 93.72 % Rotamer: Outliers : 2.81 % Allowed : 20.56 % Favored : 76.63 % 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: 1.33 (0.22), residues: 632 sheet: -0.25 (0.56), residues: 78 loop : -2.87 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 979 TYR 0.014 0.001 TYR A 717 PHE 0.017 0.001 PHE A 776 TRP 0.009 0.001 TRP A 510 HIS 0.004 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (15402) covalent geometry : angle 0.54895 / 0.27 (22053) SS BOND : bond 0.01518 / 1.07 ( 2) SS BOND : angle 1.87646 / 1.07 ( 4) hydrogen bonds : bond 0.04114 / 2.69 ( 603) hydrogen bonds : angle 3.77782 / 2.68 ( 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 107 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 VAL cc_start: 0.6969 (t) cc_final: 0.6607 (m) REVERT: A 327 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7644 (pm20) REVERT: A 332 LEU cc_start: 0.8236 (mt) cc_final: 0.7840 (mt) REVERT: A 452 LEU cc_start: 0.9348 (mt) cc_final: 0.8768 (pp) REVERT: A 922 MET cc_start: 0.7147 (pmm) cc_final: 0.6772 (ptt) outliers start: 28 outliers final: 25 residues processed: 97 average time/residue: 0.1114 time to fit residues: 16.8220 Evaluate side-chains 101 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 500 HIS Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 706 LEU 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 845 CYS Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain K residue 31 HIS 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 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: 0.0670 chunk 80 optimal weight: 0.8980 chunk 5 optimal weight: 0.0970 chunk 137 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 33 optimal weight: 0.0060 chunk 13 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 overall best weight: 0.3332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.107407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.078739 restraints weight = 83955.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.080173 restraints weight = 45984.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.080661 restraints weight = 33003.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.081746 restraints weight = 29055.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.082025 restraints weight = 26613.854| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 15404 Z= 0.102 Angle : 0.558 13.097 22057 Z= 0.268 Chirality : 0.033 0.298 2688 Planarity : 0.004 0.054 1895 Dihedral : 13.079 170.696 4290 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.68 % Favored : 94.23 % Rotamer: Outliers : 2.91 % Allowed : 20.66 % 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: -0.43 (0.26), residues: 1162 helix: 1.32 (0.22), residues: 632 sheet: -0.13 (0.57), residues: 78 loop : -2.82 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 979 TYR 0.014 0.001 TYR A 717 PHE 0.033 0.001 PHE A 812 TRP 0.008 0.001 TRP A 510 HIS 0.004 0.001 HIS A 815 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (15402) covalent geometry : angle 0.55784 / 0.27 (22053) SS BOND : bond 0.01328 / 0.94 ( 2) SS BOND : angle 1.82306 / 1.02 ( 4) hydrogen bonds : bond 0.03959 / 2.58 ( 603) hydrogen bonds : angle 3.77321 / 2.68 ( 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 106 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 VAL cc_start: 0.7059 (t) cc_final: 0.6693 (m) REVERT: A 327 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7638 (pm20) REVERT: A 332 LEU cc_start: 0.8225 (mt) cc_final: 0.7834 (mt) REVERT: A 452 LEU cc_start: 0.9345 (mt) cc_final: 0.8736 (pp) REVERT: A 922 MET cc_start: 0.7122 (pmm) cc_final: 0.6829 (ptt) outliers start: 29 outliers final: 25 residues processed: 95 average time/residue: 0.1085 time to fit residues: 15.7959 Evaluate side-chains 102 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 500 HIS Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 686 ILE 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 794 GLN Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain K residue 31 HIS 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 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: 0.7980 chunk 24 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 chunk 27 optimal weight: 0.4980 chunk 78 optimal weight: 0.6980 chunk 120 optimal weight: 8.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.107107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.077875 restraints weight = 84122.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.079746 restraints weight = 45831.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.080589 restraints weight = 33743.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.081304 restraints weight = 29345.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.081500 restraints weight = 27197.481| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 15404 Z= 0.103 Angle : 0.550 13.685 22057 Z= 0.262 Chirality : 0.033 0.295 2688 Planarity : 0.004 0.067 1895 Dihedral : 13.057 170.858 4290 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.77 % Favored : 94.15 % Rotamer: Outliers : 2.71 % Allowed : 20.66 % Favored : 76.63 % 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: -0.37 (0.26), residues: 1162 helix: 1.37 (0.22), residues: 631 sheet: 0.10 (0.59), residues: 77 loop : -2.81 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 979 TYR 0.014 0.001 TYR A 717 PHE 0.022 0.001 PHE A 812 TRP 0.008 0.001 TRP A 519 HIS 0.005 0.001 HIS A 762 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (15402) covalent geometry : angle 0.55002 / 0.26 (22053) SS BOND : bond 0.01378 / 0.97 ( 2) SS BOND : angle 1.74386 / 1.02 ( 4) hydrogen bonds : bond 0.03952 / 2.58 ( 603) hydrogen bonds : angle 3.73547 / 2.66 ( 1643) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3635.92 seconds wall clock time: 62 minutes 59.41 seconds (3779.41 seconds total)