Starting phenix.real_space_refine on Thu Aug 6 05:04:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8smw_40604/08_2026/8smw_40604.cif Found real_map, /net/cci-nas-00/data/ceres_data/8smw_40604/08_2026/8smw_40604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8smw_40604/08_2026/8smw_40604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8smw_40604/08_2026/8smw_40604.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8smw_40604/08_2026/8smw_40604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8smw_40604/08_2026/8smw_40604.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8smw_40604/08_2026/8smw_40604.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8smw_40604/08_2026/8smw_40604.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.105 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 294 5.49 5 S 32 5.16 5 C 7891 2.51 5 N 2608 2.21 5 O 3171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13998 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 740 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 728 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Conformer: "B" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} bond proxies already assigned to first conformer: 698 Chain: "L" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1188 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12296 SG CYS K 31 34.563 67.474 43.721 1.00 33.88 S ATOM 12446 SG CYS K 51 32.713 64.181 43.621 1.00 29.69 S ATOM 12470 SG CYS K 54 34.556 65.439 40.531 1.00 35.60 S ATOM 12187 SG CYS K 16 22.929 63.352 48.998 1.00 58.51 S ATOM 12205 SG CYS K 19 20.440 61.444 50.962 1.00 60.46 S ATOM 12335 SG CYS K 36 23.193 63.501 52.800 1.00 47.61 S ATOM 12357 SG CYS K 39 24.103 60.352 51.278 1.00 48.10 S Time building chain proxies: 2.32, per 1000 atoms: 0.17 Number of scatterers: 13998 At special positions: 0 Unit cell: (108.896, 130.144, 128.816, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 32 16.00 P 294 15.00 O 3171 8.00 N 2608 7.00 C 7891 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " SER C 11 " - " SER D 123 " " SER G 11 " - " SER H 123 " Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 320.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 33 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " Number of angles added : 9 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1888 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 12 sheets defined 64.2% alpha, 4.5% beta 136 base pairs and 255 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.615A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.783A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.043A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.504A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.553A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.749A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.692A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 4.069A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.690A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.851A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.618A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.579A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 72 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.571A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.549A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.760A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 47 Processing helix chain 'K' and resid 58 through 67 removed outlier: 3.841A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 removed outlier: 3.661A pdb=" N TRP K 77 " --> pdb=" O ASN K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 91 removed outlier: 4.377A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS K 89 " --> pdb=" O PRO K 85 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU K 90 " --> pdb=" O ARG K 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 16 removed outlier: 3.811A pdb=" N ARG L 5 " --> pdb=" O MET L 1 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP L 16 " --> pdb=" O ASP L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 112 removed outlier: 3.568A pdb=" N LEU L 110 " --> pdb=" O ILE L 106 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP L 111 " --> pdb=" O ALA L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 130 Processing helix chain 'L' and resid 130 through 146 removed outlier: 3.548A pdb=" N TYR L 134 " --> pdb=" O ASP L 130 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS L 144 " --> pdb=" O GLU L 140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.940A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.625A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.542A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.860A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.101A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.714A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 removed outlier: 3.536A pdb=" N ILE G 78 " --> pdb=" O GLY H 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 26 through 28 Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 25 464 hydrogen bonds defined for protein. 1374 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 349 hydrogen bonds 694 hydrogen bond angles 0 basepair planarities 136 basepair parallelities 255 stacking parallelities Total time for adding SS restraints: 2.30 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2994 1.33 - 1.46: 4511 1.46 - 1.58: 6726 1.58 - 1.70: 586 1.70 - 1.82: 47 Bond restraints: 14864 Sorted by residual: bond pdb=" C3' DT J -67 " pdb=" C2' DT J -67 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DG J 21 " pdb=" C2' DG J 21 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DC I 21 " pdb=" C2' DC I 21 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DT J -17 " pdb=" C2' DT J -17 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DA J -73 " pdb=" C2' DA J -73 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.96e+00 ... (remaining 14859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 20399 1.69 - 3.39: 928 3.39 - 5.08: 23 5.08 - 6.77: 2 6.77 - 8.46: 1 Bond angle restraints: 21353 Sorted by residual: angle pdb=" O4' DT I -26 " pdb=" C4' DT I -26 " pdb=" C3' DT I -26 " ideal model delta sigma weight residual 106.00 103.11 2.89 6.00e-01 2.78e+00 2.32e+01 angle pdb=" N3 DT J -24 " pdb=" C4 DT J -24 " pdb=" O4 DT J -24 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT I -43 " pdb=" C4 DT I -43 " pdb=" O4 DT I -43 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT I 38 " pdb=" C4 DT I 38 " pdb=" O4 DT I 38 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT I -17 " pdb=" C4 DT I -17 " pdb=" O4 DT I -17 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 ... (remaining 21348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 6856 35.68 - 71.37: 1354 71.37 - 107.05: 18 107.05 - 142.74: 0 142.74 - 178.42: 2 Dihedral angle restraints: 8230 sinusoidal: 5306 harmonic: 2924 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 38.42 -178.42 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 71.12 148.88 1 3.50e+01 8.16e-04 1.45e+01 dihedral pdb=" CG ARG F 67 " pdb=" CD ARG F 67 " pdb=" NE ARG F 67 " pdb=" CZ ARG F 67 " ideal model delta sinusoidal sigma weight residual 90.00 134.35 -44.35 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 8227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1289 0.028 - 0.057: 686 0.057 - 0.085: 286 0.085 - 0.114: 138 0.114 - 0.142: 20 Chirality restraints: 2419 Sorted by residual: chirality pdb=" C3' DG J -70 " pdb=" C4' DG J -70 " pdb=" O3' DG J -70 " pdb=" C2' DG J -70 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA VAL K 24 " pdb=" N VAL K 24 " pdb=" C VAL K 24 " pdb=" CB VAL K 24 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 2416 not shown) Planarity restraints: 1690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " -0.026 2.00e-02 2.50e+03 1.13e-02 3.50e+00 pdb=" N9 DA I -35 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " -0.022 2.00e-02 2.50e+03 9.01e-03 2.44e+00 pdb=" N9 DG I 47 " 0.019 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 107 " -0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" C ALA D 107 " 0.024 2.00e-02 2.50e+03 pdb=" O ALA D 107 " -0.009 2.00e-02 2.50e+03 pdb=" N LYS D 108 " -0.008 2.00e-02 2.50e+03 ... (remaining 1687 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 368 2.68 - 3.23: 11841 3.23 - 3.79: 24083 3.79 - 4.34: 32108 4.34 - 4.90: 47074 Nonbonded interactions: 115474 Sorted by model distance: nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.124 2.496 nonbonded pdb=" O ASN G 73 " pdb=" ND2 ASN G 73 " model vdw 2.244 3.120 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.257 3.040 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.268 3.040 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.305 3.040 ... (remaining 115469 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.290 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 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 : 0.005 0.037 14874 Z= 0.476 Angle : 0.698 8.463 21368 Z= 0.606 Chirality : 0.043 0.142 2419 Planarity : 0.004 0.035 1688 Dihedral : 26.233 178.423 6336 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.72 (0.27), residues: 983 helix: 2.18 (0.21), residues: 625 sheet: 0.52 (1.01), residues: 24 loop : -0.86 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 125 TYR 0.009 0.001 TYR F 51 PHE 0.009 0.001 PHE L 62 TRP 0.008 0.001 TRP K 61 HIS 0.003 0.001 HIS L 0 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.48 (14864) covalent geometry : angle 0.69310 / 0.61 (21353) hydrogen bonds : bond 0.11039 / 7.28 ( 813) hydrogen bonds : angle 4.07863 / 2.97 ( 2068) metal coordination : bond 0.00473 / 0.24 ( 8) metal coordination : angle 4.06902 / 2.12 ( 9) link_TRANS : bond 0.00156 / 0.08 ( 2) link_TRANS : angle 0.56251 / 0.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.286 Fit side-chains REVERT: C 73 ASN cc_start: 0.7713 (m-40) cc_final: 0.7270 (t0) REVERT: D 99 ARG cc_start: 0.7840 (mtt-85) cc_final: 0.7445 (mtm-85) REVERT: H 46 LYS cc_start: 0.8702 (mmtt) cc_final: 0.8435 (mmtt) REVERT: H 79 ARG cc_start: 0.8895 (ttm110) cc_final: 0.8512 (ttm170) REVERT: H 99 ARG cc_start: 0.7930 (mtt-85) cc_final: 0.7496 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1498 time to fit residues: 22.0740 Evaluate side-chains 98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0370 chunk 51 optimal weight: 0.3980 chunk 117 optimal weight: 2.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN D 47 GLN F 25 ASN L 7 ASN L 92 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.159699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.105352 restraints weight = 30051.369| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.95 r_work: 0.2755 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.0575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14874 Z= 0.138 Angle : 0.585 7.376 21368 Z= 0.343 Chirality : 0.043 0.239 2419 Planarity : 0.004 0.037 1688 Dihedral : 29.370 176.552 4332 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.70 % Allowed : 4.79 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.96 (0.27), residues: 983 helix: 2.44 (0.21), residues: 628 sheet: 0.50 (1.01), residues: 24 loop : -0.96 (0.31), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 125 TYR 0.007 0.001 TYR F 51 PHE 0.009 0.001 PHE L 62 TRP 0.009 0.001 TRP K 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.14 (14864) covalent geometry : angle 0.57963 / 0.34 (21353) hydrogen bonds : bond 0.05790 / 3.94 ( 813) hydrogen bonds : angle 3.31038 / 2.44 ( 2068) metal coordination : bond 0.00454 / 0.23 ( 8) metal coordination : angle 3.98782 / 2.09 ( 9) link_TRANS : bond 0.00043 / 0.02 ( 2) link_TRANS : angle 0.33464 / 0.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.271 Fit side-chains REVERT: C 73 ASN cc_start: 0.7489 (m-40) cc_final: 0.6818 (t0) REVERT: D 99 ARG cc_start: 0.8290 (mtt-85) cc_final: 0.7738 (mtm-85) REVERT: H 99 ARG cc_start: 0.8279 (mtt-85) cc_final: 0.7603 (mtm180) REVERT: L 7 ASN cc_start: 0.8567 (m-40) cc_final: 0.8227 (m110) REVERT: L 30 MET cc_start: 0.5759 (mmm) cc_final: 0.5464 (mmm) outliers start: 6 outliers final: 4 residues processed: 107 average time/residue: 0.1492 time to fit residues: 21.3782 Evaluate side-chains 101 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 123 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 85 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 110 optimal weight: 0.0770 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN B 93 GLN L 92 GLN L 135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.158040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.101974 restraints weight = 25791.920| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.82 r_work: 0.2736 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.0747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14874 Z= 0.136 Angle : 0.560 7.434 21368 Z= 0.330 Chirality : 0.042 0.247 2419 Planarity : 0.004 0.037 1688 Dihedral : 29.397 177.160 4332 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.70 % Allowed : 7.01 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.12 (0.27), residues: 983 helix: 2.59 (0.21), residues: 628 sheet: 0.54 (1.02), residues: 24 loop : -0.95 (0.31), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 125 TYR 0.007 0.001 TYR F 51 PHE 0.011 0.001 PHE L 50 TRP 0.009 0.001 TRP K 61 HIS 0.002 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.14 (14864) covalent geometry : angle 0.55450 / 0.33 (21353) hydrogen bonds : bond 0.05370 / 3.62 ( 813) hydrogen bonds : angle 3.15002 / 2.32 ( 2068) metal coordination : bond 0.00463 / 0.23 ( 8) metal coordination : angle 3.98134 / 2.07 ( 9) link_TRANS : bond 0.00040 / 0.02 ( 2) link_TRANS : angle 0.24281 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.309 Fit side-chains REVERT: C 73 ASN cc_start: 0.7335 (m-40) cc_final: 0.6765 (t0) REVERT: D 99 ARG cc_start: 0.8251 (mtt-85) cc_final: 0.7716 (mtm-85) REVERT: H 99 ARG cc_start: 0.8290 (mtt-85) cc_final: 0.7623 (mtm180) REVERT: L 7 ASN cc_start: 0.8748 (m-40) cc_final: 0.8318 (m110) REVERT: L 8 LYS cc_start: 0.8378 (mmmm) cc_final: 0.8073 (mmtt) REVERT: L 30 MET cc_start: 0.5336 (mmm) cc_final: 0.5007 (mmm) REVERT: L 147 MET cc_start: 0.6746 (ptp) cc_final: 0.6443 (ptp) outliers start: 6 outliers final: 4 residues processed: 100 average time/residue: 0.1348 time to fit residues: 18.5167 Evaluate side-chains 97 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 75 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 68 optimal weight: 0.5980 chunk 23 optimal weight: 0.0060 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 119 optimal weight: 0.2980 chunk 106 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN G 24 GLN L 92 GLN L 135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.159682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.104752 restraints weight = 20613.816| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.45 r_work: 0.2762 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14874 Z= 0.148 Angle : 0.574 7.777 21368 Z= 0.332 Chirality : 0.043 0.261 2419 Planarity : 0.004 0.036 1688 Dihedral : 29.530 176.995 4332 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.93 % Allowed : 8.41 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.11 (0.27), residues: 983 helix: 2.59 (0.21), residues: 626 sheet: 0.65 (1.07), residues: 24 loop : -0.97 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 129 TYR 0.008 0.001 TYR F 51 PHE 0.011 0.002 PHE L 50 TRP 0.009 0.001 TRP K 61 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (14864) covalent geometry : angle 0.56762 / 0.33 (21353) hydrogen bonds : bond 0.05656 / 3.80 ( 813) hydrogen bonds : angle 3.10373 / 2.27 ( 2068) metal coordination : bond 0.00495 / 0.25 ( 8) metal coordination : angle 4.08262 / 2.09 ( 9) link_TRANS : bond 0.00014 / 0.01 ( 2) link_TRANS : angle 0.20481 / 0.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.309 Fit side-chains REVERT: C 73 ASN cc_start: 0.7425 (m-40) cc_final: 0.6861 (t0) REVERT: D 99 ARG cc_start: 0.8313 (mtt-85) cc_final: 0.7757 (mtm-85) REVERT: H 99 ARG cc_start: 0.8382 (mtt-85) cc_final: 0.7664 (mtm180) REVERT: L 7 ASN cc_start: 0.8697 (m-40) cc_final: 0.8191 (m110) REVERT: L 30 MET cc_start: 0.5401 (mmm) cc_final: 0.5012 (mmm) REVERT: L 147 MET cc_start: 0.6767 (ptp) cc_final: 0.6479 (ptp) outliers start: 8 outliers final: 5 residues processed: 94 average time/residue: 0.1440 time to fit residues: 18.3611 Evaluate side-chains 93 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 17 optimal weight: 0.0970 chunk 61 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 113 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.155710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.102563 restraints weight = 29082.612| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.87 r_work: 0.2707 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14874 Z= 0.132 Angle : 0.565 7.551 21368 Z= 0.327 Chirality : 0.042 0.250 2419 Planarity : 0.004 0.037 1688 Dihedral : 29.517 177.087 4332 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.82 % Allowed : 9.11 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.17 (0.27), residues: 983 helix: 2.64 (0.21), residues: 627 sheet: 0.68 (1.07), residues: 24 loop : -0.96 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 129 TYR 0.007 0.001 TYR F 51 PHE 0.009 0.001 PHE L 62 TRP 0.009 0.001 TRP K 61 HIS 0.002 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.13 (14864) covalent geometry : angle 0.55889 / 0.33 (21353) hydrogen bonds : bond 0.05439 / 3.66 ( 813) hydrogen bonds : angle 3.08960 / 2.28 ( 2068) metal coordination : bond 0.00454 / 0.23 ( 8) metal coordination : angle 3.95997 / 2.05 ( 9) link_TRANS : bond 0.00039 / 0.02 ( 2) link_TRANS : angle 0.22676 / 0.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.246 Fit side-chains REVERT: C 73 ASN cc_start: 0.7379 (m-40) cc_final: 0.6861 (t0) REVERT: D 99 ARG cc_start: 0.8237 (mtt-85) cc_final: 0.7703 (mtm-85) REVERT: H 99 ARG cc_start: 0.8305 (mtt-85) cc_final: 0.7616 (mtm180) REVERT: L 30 MET cc_start: 0.5361 (mmm) cc_final: 0.4960 (mmm) REVERT: L 147 MET cc_start: 0.6658 (ptp) cc_final: 0.6367 (ptp) outliers start: 7 outliers final: 6 residues processed: 94 average time/residue: 0.1370 time to fit residues: 17.6332 Evaluate side-chains 95 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 24 optimal weight: 1.9990 chunk 99 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 72 optimal weight: 30.0000 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 80 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN L 135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.151123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.095567 restraints weight = 21051.878| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.46 r_work: 0.2669 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14874 Z= 0.180 Angle : 0.624 8.474 21368 Z= 0.349 Chirality : 0.046 0.276 2419 Planarity : 0.004 0.035 1688 Dihedral : 29.795 177.125 4332 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.17 % Allowed : 8.88 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.84 (0.27), residues: 983 helix: 2.40 (0.21), residues: 625 sheet: 0.53 (1.03), residues: 24 loop : -1.12 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 79 TYR 0.012 0.002 TYR C 50 PHE 0.017 0.002 PHE L 50 TRP 0.010 0.002 TRP K 61 HIS 0.005 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (14864) covalent geometry : angle 0.61825 / 0.35 (21353) hydrogen bonds : bond 0.06573 / 4.42 ( 813) hydrogen bonds : angle 3.22836 / 2.36 ( 2068) metal coordination : bond 0.00654 / 0.33 ( 8) metal coordination : angle 4.35362 / 2.21 ( 9) link_TRANS : bond 0.00058 / 0.03 ( 2) link_TRANS : angle 0.26339 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.291 Fit side-chains REVERT: A 81 ASP cc_start: 0.7602 (t0) cc_final: 0.7373 (t0) REVERT: C 73 ASN cc_start: 0.7627 (m-40) cc_final: 0.7096 (t0) REVERT: D 99 ARG cc_start: 0.8258 (mtt-85) cc_final: 0.7829 (mtm-85) REVERT: H 99 ARG cc_start: 0.8310 (mtt-85) cc_final: 0.7928 (mtm-85) REVERT: K 46 LYS cc_start: 0.8656 (ttmt) cc_final: 0.8413 (ttmm) REVERT: L 30 MET cc_start: 0.5573 (mmm) cc_final: 0.5172 (mmm) REVERT: L 147 MET cc_start: 0.6754 (ptp) cc_final: 0.6487 (ptp) outliers start: 10 outliers final: 7 residues processed: 96 average time/residue: 0.1340 time to fit residues: 17.3161 Evaluate side-chains 93 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 91 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.153256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.097422 restraints weight = 20533.898| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.45 r_work: 0.2720 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2540 r_free = 0.2540 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2540 r_free = 0.2540 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14874 Z= 0.155 Angle : 0.606 7.840 21368 Z= 0.340 Chirality : 0.045 0.267 2419 Planarity : 0.004 0.035 1688 Dihedral : 29.768 176.611 4332 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.93 % Allowed : 10.05 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.84 (0.27), residues: 983 helix: 2.39 (0.21), residues: 626 sheet: 0.49 (1.02), residues: 24 loop : -1.10 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 81 TYR 0.010 0.001 TYR F 51 PHE 0.013 0.002 PHE L 50 TRP 0.009 0.001 TRP K 61 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (14864) covalent geometry : angle 0.59998 / 0.34 (21353) hydrogen bonds : bond 0.06136 / 4.14 ( 813) hydrogen bonds : angle 3.21789 / 2.40 ( 2068) metal coordination : bond 0.00570 / 0.28 ( 8) metal coordination : angle 4.27190 / 2.21 ( 9) link_TRANS : bond 0.00071 / 0.04 ( 2) link_TRANS : angle 0.24514 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.316 Fit side-chains REVERT: A 81 ASP cc_start: 0.7801 (t0) cc_final: 0.7564 (t0) REVERT: C 73 ASN cc_start: 0.7585 (m-40) cc_final: 0.7028 (t0) REVERT: D 99 ARG cc_start: 0.8334 (mtt-85) cc_final: 0.7877 (mtm-85) REVERT: H 99 ARG cc_start: 0.8425 (mtt-85) cc_final: 0.8071 (mtm-85) REVERT: K 46 LYS cc_start: 0.8609 (ttmt) cc_final: 0.8376 (ttmm) REVERT: L 30 MET cc_start: 0.5569 (mmm) cc_final: 0.5159 (mmm) REVERT: L 147 MET cc_start: 0.6818 (ptp) cc_final: 0.6584 (ptp) outliers start: 8 outliers final: 7 residues processed: 91 average time/residue: 0.1386 time to fit residues: 17.0800 Evaluate side-chains 93 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 41 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 0.0570 chunk 21 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.154382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.097397 restraints weight = 26412.987| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.92 r_work: 0.2640 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14874 Z= 0.132 Angle : 0.586 7.326 21368 Z= 0.333 Chirality : 0.044 0.244 2419 Planarity : 0.004 0.037 1688 Dihedral : 29.707 177.302 4332 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.82 % Allowed : 10.51 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.01 (0.27), residues: 983 helix: 2.53 (0.21), residues: 626 sheet: 0.51 (1.02), residues: 24 loop : -1.04 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 136 TYR 0.008 0.001 TYR F 51 PHE 0.009 0.001 PHE L 62 TRP 0.008 0.001 TRP K 61 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.13 (14864) covalent geometry : angle 0.58059 / 0.33 (21353) hydrogen bonds : bond 0.05686 / 3.84 ( 813) hydrogen bonds : angle 3.15907 / 2.37 ( 2068) metal coordination : bond 0.00473 / 0.24 ( 8) metal coordination : angle 4.05184 / 2.10 ( 9) link_TRANS : bond 0.00101 / 0.05 ( 2) link_TRANS : angle 0.24654 / 0.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.340 Fit side-chains REVERT: C 73 ASN cc_start: 0.7514 (m-40) cc_final: 0.6987 (t0) REVERT: D 99 ARG cc_start: 0.8285 (mtt-85) cc_final: 0.7755 (mtm-85) REVERT: K 46 LYS cc_start: 0.8564 (ttmt) cc_final: 0.8323 (ttmm) REVERT: L 30 MET cc_start: 0.5550 (mmm) cc_final: 0.5143 (mmm) REVERT: L 147 MET cc_start: 0.6790 (ptp) cc_final: 0.6535 (ptp) outliers start: 7 outliers final: 6 residues processed: 94 average time/residue: 0.1322 time to fit residues: 16.7165 Evaluate side-chains 95 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain L residue 100 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 25 optimal weight: 0.0980 chunk 31 optimal weight: 0.8980 chunk 23 optimal weight: 0.0980 chunk 39 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.154920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.101059 restraints weight = 29135.602| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.93 r_work: 0.2668 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14874 Z= 0.134 Angle : 0.578 7.213 21368 Z= 0.330 Chirality : 0.043 0.251 2419 Planarity : 0.004 0.037 1688 Dihedral : 29.669 176.784 4332 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.70 % Allowed : 10.75 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.07 (0.27), residues: 983 helix: 2.58 (0.21), residues: 626 sheet: 0.53 (1.02), residues: 24 loop : -1.00 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 99 TYR 0.008 0.001 TYR F 51 PHE 0.010 0.001 PHE L 62 TRP 0.009 0.001 TRP K 61 HIS 0.002 0.000 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 (14864) covalent geometry : angle 0.57221 / 0.33 (21353) hydrogen bonds : bond 0.05506 / 3.72 ( 813) hydrogen bonds : angle 3.10902 / 2.33 ( 2068) metal coordination : bond 0.00484 / 0.24 ( 8) metal coordination : angle 4.05792 / 2.11 ( 9) link_TRANS : bond 0.00077 / 0.04 ( 2) link_TRANS : angle 0.26007 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.290 Fit side-chains REVERT: C 73 ASN cc_start: 0.7417 (m-40) cc_final: 0.6967 (t0) REVERT: D 99 ARG cc_start: 0.8312 (mtt-85) cc_final: 0.7803 (mtm-85) REVERT: H 99 ARG cc_start: 0.8230 (mtt-85) cc_final: 0.7580 (mtm180) REVERT: K 46 LYS cc_start: 0.8637 (ttmt) cc_final: 0.8385 (ttmm) REVERT: L 30 MET cc_start: 0.5525 (mmm) cc_final: 0.5115 (mmm) REVERT: L 147 MET cc_start: 0.6691 (ptp) cc_final: 0.6437 (ptp) outliers start: 6 outliers final: 4 residues processed: 90 average time/residue: 0.1373 time to fit residues: 16.7031 Evaluate side-chains 90 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain L residue 100 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 42 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 114 optimal weight: 0.1980 chunk 19 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.149508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.109284 restraints weight = 27435.460| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.34 r_work: 0.2604 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14874 Z= 0.139 Angle : 0.568 7.352 21368 Z= 0.326 Chirality : 0.042 0.261 2419 Planarity : 0.004 0.037 1688 Dihedral : 29.648 176.935 4332 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.70 % Allowed : 10.98 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.05 (0.27), residues: 983 helix: 2.56 (0.21), residues: 626 sheet: 0.51 (1.02), residues: 24 loop : -1.02 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 99 TYR 0.008 0.001 TYR F 51 PHE 0.013 0.001 PHE L 50 TRP 0.009 0.001 TRP K 61 HIS 0.002 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (14864) covalent geometry : angle 0.56172 / 0.33 (21353) hydrogen bonds : bond 0.05447 / 3.66 ( 813) hydrogen bonds : angle 3.09420 / 2.32 ( 2068) metal coordination : bond 0.00495 / 0.24 ( 8) metal coordination : angle 4.00428 / 2.07 ( 9) link_TRANS : bond 0.00048 / 0.02 ( 2) link_TRANS : angle 0.20751 / 0.11 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.362 Fit side-chains REVERT: C 73 ASN cc_start: 0.7532 (m-40) cc_final: 0.7264 (t0) REVERT: D 99 ARG cc_start: 0.8393 (mtt-85) cc_final: 0.7923 (mtm-85) REVERT: H 99 ARG cc_start: 0.8320 (mtt-85) cc_final: 0.7726 (mtm180) REVERT: K 46 LYS cc_start: 0.8784 (ttmt) cc_final: 0.8490 (ttmm) REVERT: L 30 MET cc_start: 0.5672 (mmm) cc_final: 0.5260 (mmm) REVERT: L 147 MET cc_start: 0.6666 (ptp) cc_final: 0.6342 (ptp) outliers start: 6 outliers final: 4 residues processed: 93 average time/residue: 0.1431 time to fit residues: 18.1528 Evaluate side-chains 93 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain L residue 100 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 54 optimal weight: 0.7980 chunk 109 optimal weight: 0.2980 chunk 25 optimal weight: 0.0570 chunk 30 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 92 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.150205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.109958 restraints weight = 21045.269| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.57 r_work: 0.2969 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14874 Z= 0.129 Angle : 0.564 7.059 21368 Z= 0.325 Chirality : 0.042 0.248 2419 Planarity : 0.004 0.037 1688 Dihedral : 29.623 177.144 4332 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.35 % Allowed : 11.45 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.12 (0.27), residues: 983 helix: 2.61 (0.21), residues: 626 sheet: 0.54 (1.03), residues: 24 loop : -1.00 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 86 TYR 0.007 0.001 TYR F 51 PHE 0.013 0.001 PHE L 50 TRP 0.009 0.001 TRP K 61 HIS 0.002 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.13 (14864) covalent geometry : angle 0.55841 / 0.32 (21353) hydrogen bonds : bond 0.05235 / 3.52 ( 813) hydrogen bonds : angle 3.06983 / 2.31 ( 2068) metal coordination : bond 0.00451 / 0.22 ( 8) metal coordination : angle 3.89488 / 2.02 ( 9) link_TRANS : bond 0.00070 / 0.03 ( 2) link_TRANS : angle 0.19715 / 0.10 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2727.36 seconds wall clock time: 47 minutes 11.33 seconds (2831.33 seconds total)