Starting phenix.real_space_refine on Wed Mar 4 16:11:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v99_31811/03_2026/7v99_31811.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v99_31811/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7v99_31811/03_2026/7v99_31811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v99_31811/03_2026/7v99_31811.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v99_31811/03_2026/7v99_31811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v99_31811/03_2026/7v99_31811.map" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.242 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 249 5.49 5 S 39 5.16 5 C 8291 2.51 5 N 2662 2.21 5 O 3341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 2.93, per 1000 atoms: 0.20 Number of scatterers: 14582 At special positions: 0 Unit cell: (148.5, 125.4, 132, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 249 15.00 O 3341 8.00 N 2662 7.00 C 8291 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 845 " - pdb=" SG CYS A 896 " distance=2.05 Simple disulfide: pdb=" SG CYS A 982 " - pdb=" SG CYS A1043 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 416.0 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: 1.68 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: 3.77 Time building geometry restraints manager: 1.65 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=" 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=" C ALA K 47 " pdb=" N PRO K 48 " ideal model delta sigma weight residual 1.336 1.356 -0.021 1.23e-02 6.61e+03 2.78e+00 bond pdb=" C LYS A 430 " pdb=" N PRO A 431 " ideal model delta sigma weight residual 1.335 1.355 -0.020 1.30e-02 5.92e+03 2.42e+00 bond pdb=" CA ASN A 799 " pdb=" CB ASN A 799 " ideal model delta sigma weight residual 1.527 1.562 -0.035 2.48e-02 1.63e+03 2.00e+00 ... (remaining 15397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 21458 1.41 - 2.82: 499 2.82 - 4.23: 66 4.23 - 5.64: 26 5.64 - 7.05: 4 Bond angle restraints: 22053 Sorted by residual: 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 angle pdb=" N ALA A 918 " pdb=" CA ALA A 918 " pdb=" C ALA A 918 " ideal model delta sigma weight residual 114.56 110.75 3.81 1.27e+00 6.20e-01 9.00e+00 angle pdb=" C VAL A 162 " pdb=" N ALA A 163 " pdb=" CA ALA A 163 " ideal model delta sigma weight residual 122.85 119.74 3.11 1.10e+00 8.26e-01 7.97e+00 angle pdb=" C LEU A1042 " pdb=" N CYS A1043 " pdb=" CA CYS A1043 " ideal model delta sigma weight residual 121.58 116.08 5.50 1.95e+00 2.63e-01 7.95e+00 angle pdb=" N VAL A1087 " pdb=" CA VAL A1087 " pdb=" C VAL A1087 " ideal model delta sigma weight residual 112.12 109.77 2.35 8.40e-01 1.42e+00 7.84e+00 ... (remaining 22048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 8983 35.43 - 70.86: 639 70.86 - 106.29: 100 106.29 - 141.72: 1 141.72 - 177.14: 4 Dihedral angle restraints: 9727 sinusoidal: 6325 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 9724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2105 0.028 - 0.057: 414 0.057 - 0.085: 106 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: 7.030 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: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.740 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 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= 0.125 Angle : 0.531 7.050 22057 Z= 0.320 Chirality : 0.028 0.142 2688 Planarity : 0.004 0.061 1895 Dihedral : 20.831 177.144 7521 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 covalent geometry : bond 0.00207 (15402) covalent geometry : angle 0.53050 (22053) SS BOND : bond 0.01457 ( 2) SS BOND : angle 1.96310 ( 4) hydrogen bonds : bond 0.18735 ( 603) hydrogen bonds : angle 7.14241 ( 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 : 0.300 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: 0.1968 time to fit residues: 45.7907 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 : 0.398 ------------------------------------------------------------------------------- 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: 5.9990 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... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 95 ASN A 490 ASN A 506 GLN ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 HIS A 906 ASN A 921 GLN A1022 HIS A1023 GLN K 31 HIS ** K 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.115810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.090191 restraints weight = 87140.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.091263 restraints weight = 45714.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.092232 restraints weight = 32005.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.092920 restraints weight = 26812.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.092920 restraints weight = 24836.675| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15404 Z= 0.120 Angle : 0.558 8.559 22057 Z= 0.273 Chirality : 0.033 0.176 2688 Planarity : 0.004 0.054 1895 Dihedral : 22.011 170.787 5262 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.94 % Favored : 93.98 % Rotamer: Outliers : 1.91 % Allowed : 12.04 % Favored : 86.06 % 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: -1.83 (0.23), residues: 1162 helix: 0.21 (0.21), residues: 616 sheet: -1.01 (0.51), residues: 76 loop : -3.31 (0.23), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 859 TYR 0.017 0.001 TYR A 667 PHE 0.015 0.001 PHE A 776 TRP 0.009 0.001 TRP A 519 HIS 0.002 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00250 (15402) covalent geometry : angle 0.55800 (22053) SS BOND : bond 0.01638 ( 2) SS BOND : angle 1.48026 ( 4) hydrogen bonds : bond 0.05513 ( 603) hydrogen bonds : angle 4.17953 ( 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 120 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.332 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: A 327 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6407 (pm20) REVERT: A 332 LEU cc_start: 0.8246 (mt) cc_final: 0.7990 (mt) REVERT: A 378 ARG cc_start: 0.5756 (ttt180) cc_final: 0.3139 (mtt180) REVERT: A 452 LEU cc_start: 0.9301 (mt) cc_final: 0.8847 (pp) REVERT: A 872 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8202 (mt) REVERT: A 979 ARG cc_start: 0.8042 (ttm-80) cc_final: 0.7708 (ttm110) outliers start: 19 outliers final: 9 residues processed: 114 average time/residue: 0.1504 time to fit residues: 23.7460 Evaluate side-chains 98 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 338 LYS 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 A residue 953 SER Chi-restraints excluded: chain A residue 1082 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: 0.6980 chunk 105 optimal weight: 10.0000 chunk 94 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 121 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 6 optimal weight: 40.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 GLN ** K 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.111648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.083003 restraints weight = 88570.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.084744 restraints weight = 46669.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.085363 restraints weight = 34404.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.086483 restraints weight = 31416.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.086483 restraints weight = 28371.219| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 15404 Z= 0.139 Angle : 0.561 11.407 22057 Z= 0.278 Chirality : 0.034 0.207 2688 Planarity : 0.004 0.044 1895 Dihedral : 21.957 169.757 5262 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.28 % Favored : 93.63 % Rotamer: Outliers : 2.31 % Allowed : 14.04 % Favored : 83.65 % 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: -1.15 (0.24), residues: 1162 helix: 0.81 (0.21), residues: 621 sheet: -0.63 (0.53), residues: 78 loop : -3.12 (0.24), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 657 TYR 0.022 0.002 TYR A 638 PHE 0.018 0.002 PHE A 708 TRP 0.009 0.001 TRP A 510 HIS 0.032 0.002 HIS K 31 Details of bonding type rmsd covalent geometry : bond 0.00300 (15402) covalent geometry : angle 0.56087 (22053) SS BOND : bond 0.01016 ( 2) SS BOND : angle 1.84977 ( 4) hydrogen bonds : bond 0.04809 ( 603) hydrogen bonds : angle 3.93237 ( 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 111 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8480 (mt) cc_final: 0.8135 (mt) REVERT: A 378 ARG cc_start: 0.5700 (ttt180) cc_final: 0.3298 (mtt180) REVERT: A 452 LEU cc_start: 0.9333 (mt) cc_final: 0.8891 (pp) REVERT: A 979 ARG cc_start: 0.8073 (ttm-80) cc_final: 0.7859 (ttm-80) REVERT: K 27 VAL cc_start: 0.6660 (m) cc_final: 0.6405 (m) outliers start: 23 outliers final: 12 residues processed: 104 average time/residue: 0.1441 time to fit residues: 21.0870 Evaluate side-chains 92 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 500 HIS Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 706 LEU 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 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: 6.9990 chunk 137 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 127 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 134 optimal weight: 8.9990 chunk 121 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 HIS A1023 GLN L 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.106296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.079057 restraints weight = 85895.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.081145 restraints weight = 47994.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.081720 restraints weight = 32197.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.080895 restraints weight = 35835.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.080744 restraints weight = 30347.553| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15404 Z= 0.176 Angle : 0.596 11.781 22057 Z= 0.302 Chirality : 0.035 0.190 2688 Planarity : 0.005 0.054 1895 Dihedral : 21.992 170.424 5262 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.88 % Favored : 93.03 % Rotamer: Outliers : 2.81 % Allowed : 16.95 % 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: -0.94 (0.25), residues: 1162 helix: 0.95 (0.21), residues: 633 sheet: -0.43 (0.56), residues: 78 loop : -3.11 (0.24), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 811 TYR 0.017 0.002 TYR A 638 PHE 0.014 0.002 PHE A 776 TRP 0.010 0.002 TRP A 371 HIS 0.012 0.002 HIS K 82 Details of bonding type rmsd covalent geometry : bond 0.00355 (15402) covalent geometry : angle 0.59504 (22053) SS BOND : bond 0.04374 ( 2) SS BOND : angle 2.32084 ( 4) hydrogen bonds : bond 0.04971 ( 603) hydrogen bonds : angle 3.98171 ( 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 113 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 VAL cc_start: 0.6885 (OUTLIER) cc_final: 0.6533 (m) REVERT: A 332 LEU cc_start: 0.8406 (mt) cc_final: 0.8097 (mt) REVERT: A 922 MET cc_start: 0.7172 (pmm) cc_final: 0.6681 (ptt) outliers start: 28 outliers final: 17 residues processed: 102 average time/residue: 0.1405 time to fit residues: 20.2894 Evaluate side-chains 92 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 500 HIS Chi-restraints excluded: chain A residue 662 PHE Chi-restraints excluded: chain A residue 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 872 LEU Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 121 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 39 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 HIS L 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.106041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.076231 restraints weight = 84279.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.078210 restraints weight = 44916.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.079335 restraints weight = 32964.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.079560 restraints weight = 28451.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.079560 restraints weight = 26815.062| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 15404 Z= 0.134 Angle : 0.558 12.194 22057 Z= 0.275 Chirality : 0.034 0.188 2688 Planarity : 0.004 0.061 1895 Dihedral : 21.930 169.668 5262 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.45 % Favored : 93.46 % Rotamer: Outliers : 2.81 % Allowed : 18.46 % 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: -0.71 (0.25), residues: 1162 helix: 1.14 (0.21), residues: 639 sheet: -0.37 (0.52), residues: 92 loop : -3.14 (0.25), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 979 TYR 0.017 0.001 TYR A 638 PHE 0.015 0.001 PHE A 776 TRP 0.010 0.001 TRP A 510 HIS 0.007 0.001 HIS K 82 Details of bonding type rmsd covalent geometry : bond 0.00292 (15402) covalent geometry : angle 0.55801 (22053) SS BOND : bond 0.02796 ( 2) SS BOND : angle 1.47208 ( 4) hydrogen bonds : bond 0.04291 ( 603) hydrogen bonds : angle 3.77352 ( 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 110 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 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: A 324 VAL cc_start: 0.7017 (t) cc_final: 0.6651 (m) REVERT: A 332 LEU cc_start: 0.8345 (mt) cc_final: 0.7998 (mt) REVERT: A 922 MET cc_start: 0.7240 (pmm) cc_final: 0.7020 (ptt) outliers start: 28 outliers final: 18 residues processed: 100 average time/residue: 0.1245 time to fit residues: 18.5679 Evaluate side-chains 92 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 500 HIS 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 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 L residue 44 VAL Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 121 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 chunk 81 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 18 optimal weight: 0.0000 chunk 31 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4444 r_free = 0.4444 target = 0.106356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.076944 restraints weight = 82832.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.078889 restraints weight = 44976.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.079974 restraints weight = 32401.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.080137 restraints weight = 27934.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.080437 restraints weight = 26629.968| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15404 Z= 0.105 Angle : 0.538 12.420 22057 Z= 0.261 Chirality : 0.033 0.201 2688 Planarity : 0.004 0.049 1895 Dihedral : 21.844 169.943 5262 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.59 % Favored : 94.32 % Rotamer: Outliers : 2.51 % Allowed : 19.76 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.25), residues: 1162 helix: 1.17 (0.21), residues: 636 sheet: -0.42 (0.57), residues: 86 loop : -2.99 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 774 TYR 0.015 0.001 TYR A 638 PHE 0.018 0.001 PHE A 776 TRP 0.007 0.001 TRP A 510 HIS 0.004 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00222 (15402) covalent geometry : angle 0.53705 (22053) SS BOND : bond 0.01409 ( 2) SS BOND : angle 1.75102 ( 4) hydrogen bonds : bond 0.04110 ( 603) hydrogen bonds : angle 3.75886 ( 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 104 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 VAL cc_start: 0.7097 (t) cc_final: 0.6752 (m) REVERT: A 332 LEU cc_start: 0.8373 (mt) cc_final: 0.7994 (mt) REVERT: A 452 LEU cc_start: 0.9306 (mt) cc_final: 0.8737 (pp) REVERT: A 922 MET cc_start: 0.7325 (pmm) cc_final: 0.7102 (ptt) outliers start: 25 outliers final: 19 residues processed: 95 average time/residue: 0.1143 time to fit residues: 16.4618 Evaluate side-chains 93 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 665 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 845 CYS 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 953 SER Chi-restraints excluded: chain A residue 974 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 28 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 75 optimal weight: 0.0370 chunk 60 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 132 optimal weight: 7.9990 chunk 135 optimal weight: 7.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.104818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.075950 restraints weight = 82521.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.077320 restraints weight = 45242.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.078313 restraints weight = 32327.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.078517 restraints weight = 27729.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.078970 restraints weight = 26315.248| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15404 Z= 0.121 Angle : 0.550 13.728 22057 Z= 0.267 Chirality : 0.033 0.205 2688 Planarity : 0.004 0.047 1895 Dihedral : 21.804 170.525 5262 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.68 % Favored : 94.23 % Rotamer: Outliers : 2.81 % Allowed : 20.16 % Favored : 77.03 % 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: 636 sheet: -0.53 (0.53), residues: 96 loop : -2.93 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 378 TYR 0.016 0.001 TYR A 638 PHE 0.014 0.001 PHE A 776 TRP 0.007 0.001 TRP A 547 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00256 (15402) covalent geometry : angle 0.54970 (22053) SS BOND : bond 0.01361 ( 2) SS BOND : angle 1.92080 ( 4) hydrogen bonds : bond 0.04193 ( 603) hydrogen bonds : angle 3.71753 ( 1643) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8354 (mt) cc_final: 0.8015 (mt) REVERT: A 690 TRP cc_start: 0.8585 (OUTLIER) cc_final: 0.8236 (t60) REVERT: A 774 ARG cc_start: 0.8398 (ttt180) cc_final: 0.8146 (tpt90) outliers start: 28 outliers final: 22 residues processed: 98 average time/residue: 0.1255 time to fit residues: 18.0767 Evaluate side-chains 98 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 500 HIS Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 690 TRP 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 87 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 13 optimal weight: 20.0000 chunk 109 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 126 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4422 r_free = 0.4422 target = 0.104561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.075578 restraints weight = 82872.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.077001 restraints weight = 45456.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.077901 restraints weight = 32398.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.078217 restraints weight = 27895.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.078217 restraints weight = 26432.584| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15404 Z= 0.115 Angle : 0.551 13.451 22057 Z= 0.265 Chirality : 0.033 0.185 2688 Planarity : 0.004 0.050 1895 Dihedral : 21.781 170.557 5262 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.77 % Favored : 94.15 % Rotamer: Outliers : 2.51 % Allowed : 20.56 % 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: -0.40 (0.25), residues: 1162 helix: 1.34 (0.22), residues: 640 sheet: -0.52 (0.52), residues: 96 loop : -2.86 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 91 TYR 0.014 0.001 TYR A 638 PHE 0.015 0.001 PHE A 776 TRP 0.007 0.001 TRP A 547 HIS 0.005 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00246 (15402) covalent geometry : angle 0.55071 (22053) SS BOND : bond 0.01551 ( 2) SS BOND : angle 2.11948 ( 4) hydrogen bonds : bond 0.04068 ( 603) hydrogen bonds : angle 3.69451 ( 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 100 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8429 (mt) cc_final: 0.8069 (mt) REVERT: A 389 MET cc_start: 0.7933 (mtm) cc_final: 0.7598 (mtm) REVERT: A 690 TRP cc_start: 0.8623 (OUTLIER) cc_final: 0.8190 (t60) REVERT: A 774 ARG cc_start: 0.8507 (ttt180) cc_final: 0.8237 (tpt90) outliers start: 25 outliers final: 21 residues processed: 90 average time/residue: 0.1327 time to fit residues: 17.5444 Evaluate side-chains 95 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 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 665 LEU Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 690 TRP 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 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 974 LEU Chi-restraints excluded: chain A residue 997 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 116 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 6 optimal weight: 0.0170 chunk 33 optimal weight: 0.8980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4420 r_free = 0.4420 target = 0.104524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.075298 restraints weight = 82940.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.076973 restraints weight = 45055.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.077460 restraints weight = 32512.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.078473 restraints weight = 28708.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.078698 restraints weight = 26351.667| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.5758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15404 Z= 0.106 Angle : 0.546 13.445 22057 Z= 0.261 Chirality : 0.032 0.197 2688 Planarity : 0.004 0.066 1895 Dihedral : 21.753 171.937 5262 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.08 % Favored : 94.84 % Rotamer: Outliers : 2.71 % Allowed : 20.76 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.26), residues: 1162 helix: 1.36 (0.22), residues: 640 sheet: -0.39 (0.58), residues: 80 loop : -2.72 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 971 TYR 0.013 0.001 TYR A 638 PHE 0.015 0.001 PHE A 776 TRP 0.007 0.001 TRP A 137 HIS 0.005 0.001 HIS K 82 Details of bonding type rmsd covalent geometry : bond 0.00227 (15402) covalent geometry : angle 0.54539 (22053) SS BOND : bond 0.01396 ( 2) SS BOND : angle 1.70079 ( 4) hydrogen bonds : bond 0.04024 ( 603) hydrogen bonds : angle 3.64839 ( 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 100 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8422 (mt) cc_final: 0.8105 (mt) REVERT: A 690 TRP cc_start: 0.8656 (OUTLIER) cc_final: 0.8155 (t60) REVERT: A 729 ILE cc_start: 0.9098 (mm) cc_final: 0.8784 (mt) REVERT: A 774 ARG cc_start: 0.8548 (ttt180) cc_final: 0.8309 (tpt90) outliers start: 27 outliers final: 19 residues processed: 91 average time/residue: 0.1210 time to fit residues: 16.2930 Evaluate side-chains 88 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 346 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 664 VAL Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 690 TRP 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 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 997 VAL Chi-restraints excluded: chain L residue 44 VAL 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: 2.9990 chunk 80 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 687 HIS ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.099746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.069522 restraints weight = 82248.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.071325 restraints weight = 44961.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.072299 restraints weight = 33576.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.072562 restraints weight = 29372.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.073023 restraints weight = 27885.213| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.6615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15404 Z= 0.221 Angle : 0.691 14.541 22057 Z= 0.339 Chirality : 0.037 0.214 2688 Planarity : 0.005 0.051 1895 Dihedral : 22.012 172.268 5262 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.14 % Favored : 92.77 % Rotamer: Outliers : 2.61 % Allowed : 21.26 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.25), residues: 1162 helix: 1.01 (0.21), residues: 643 sheet: -0.34 (0.55), residues: 97 loop : -2.81 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 470 TYR 0.015 0.002 TYR A 168 PHE 0.017 0.002 PHE A 487 TRP 0.008 0.002 TRP A 519 HIS 0.012 0.002 HIS A 500 Details of bonding type rmsd covalent geometry : bond 0.00464 (15402) covalent geometry : angle 0.69045 (22053) SS BOND : bond 0.02100 ( 2) SS BOND : angle 2.45951 ( 4) hydrogen bonds : bond 0.05377 ( 603) hydrogen bonds : angle 4.03032 ( 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 92 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8356 (mt) cc_final: 0.8066 (mt) REVERT: A 389 MET cc_start: 0.7915 (mtm) cc_final: 0.7502 (ttm) REVERT: A 690 TRP cc_start: 0.8860 (OUTLIER) cc_final: 0.8252 (t60) REVERT: L 54 ILE cc_start: 0.8011 (pt) cc_final: 0.7780 (mm) outliers start: 26 outliers final: 22 residues processed: 86 average time/residue: 0.1202 time to fit residues: 15.3319 Evaluate side-chains 88 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 690 TRP Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 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 997 VAL Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 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: 0.6980 chunk 24 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 10 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 75 optimal weight: 0.0270 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 HIS ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN A1023 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.102590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.072811 restraints weight = 83138.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.074741 restraints weight = 44125.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.075984 restraints weight = 32296.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.076208 restraints weight = 27625.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 70)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.076734 restraints weight = 26186.200| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.6541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15404 Z= 0.107 Angle : 0.580 17.481 22057 Z= 0.274 Chirality : 0.033 0.190 2688 Planarity : 0.004 0.051 1895 Dihedral : 21.840 172.177 5262 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.42 % Favored : 94.49 % Rotamer: Outliers : 2.11 % Allowed : 22.07 % Favored : 75.83 % 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: -0.39 (0.26), residues: 1162 helix: 1.33 (0.22), residues: 636 sheet: -0.31 (0.56), residues: 92 loop : -2.82 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 971 TYR 0.013 0.001 TYR A 168 PHE 0.014 0.001 PHE A 776 TRP 0.009 0.001 TRP A 547 HIS 0.006 0.001 HIS A 500 Details of bonding type rmsd covalent geometry : bond 0.00227 (15402) covalent geometry : angle 0.57937 (22053) SS BOND : bond 0.01516 ( 2) SS BOND : angle 1.61787 ( 4) hydrogen bonds : bond 0.04157 ( 603) hydrogen bonds : angle 3.77818 ( 1643) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4037.63 seconds wall clock time: 69 minutes 36.35 seconds (4176.35 seconds total)