Starting phenix.real_space_refine on Fri Jul 3 10:24:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8smw_40604/07_2026/8smw_40604.cif Found real_map, /net/cci-nas-00/data/ceres_data/8smw_40604/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8smw_40604/07_2026/8smw_40604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8smw_40604/07_2026/8smw_40604.map" model { file = "/net/cci-nas-00/data/ceres_data/8smw_40604/07_2026/8smw_40604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8smw_40604/07_2026/8smw_40604.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8smw_40604/07_2026/8smw_40604.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8smw_40604/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.90, per 1000 atoms: 0.21 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: 0.72 Conformation dependent library (CDL) restraints added in 374.3 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: 1.85 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: 2.18 Time building geometry restraints manager: 0.99 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: 20419 1.69 - 3.39: 908 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: 1.450 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: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.970 Find NCS groups from input model: 0.180 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.090 ------------------------------------------------------------------------------- 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 : 0.691 8.463 21368 Z= 0.601 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 0.68625 / 0.60 (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 : 0.353 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: 0.1515 time to fit residues: 22.3882 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 : 0.238 ------------------------------------------------------------------------------- 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: 9.9990 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 = 0.159689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.104898 restraints weight = 30059.442| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.00 r_work: 0.2758 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.0581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14874 Z= 0.142 Angle : 0.575 7.366 21368 Z= 0.341 Chirality : 0.042 0.219 2419 Planarity : 0.004 0.037 1688 Dihedral : 29.421 176.240 4332 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.56 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: 1.95 (0.27), residues: 983 helix: 2.43 (0.21), residues: 629 sheet: 0.50 (1.01), residues: 24 loop : -0.97 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 125 TYR 0.007 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 F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.14 (14864) covalent geometry : angle 0.56974 / 0.34 (21353) hydrogen bonds : bond 0.05735 / 3.91 ( 813) hydrogen bonds : angle 3.30666 / 2.44 ( 2068) metal coordination : bond 0.00462 / 0.23 ( 8) metal coordination : angle 3.98243 / 2.08 ( 9) link_TRANS : bond 0.00053 / 0.03 ( 2) link_TRANS : angle 0.32540 / 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 : 0.330 Fit side-chains REVERT: C 73 ASN cc_start: 0.7474 (m-40) cc_final: 0.6802 (t0) REVERT: D 99 ARG cc_start: 0.8297 (mtt-85) cc_final: 0.7747 (mtm-85) REVERT: H 99 ARG cc_start: 0.8298 (mtt-85) cc_final: 0.7613 (mtm180) REVERT: L 7 ASN cc_start: 0.8555 (m-40) cc_final: 0.8221 (m110) REVERT: L 30 MET cc_start: 0.5754 (mmm) cc_final: 0.5453 (mmm) outliers start: 6 outliers final: 4 residues processed: 107 average time/residue: 0.1347 time to fit residues: 19.5958 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 : 0.344 ------------------------------------------------------------------------------- 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: 4.9990 chunk 117 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 110 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.154126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.099615 restraints weight = 25839.369| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.77 r_work: 0.2685 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.0793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14874 Z= 0.167 Angle : 0.584 8.210 21368 Z= 0.339 Chirality : 0.043 0.245 2419 Planarity : 0.004 0.036 1688 Dihedral : 29.613 176.425 4332 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.70 % Allowed : 7.36 % Favored : 91.94 % 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: 1.90 (0.27), residues: 983 helix: 2.43 (0.21), residues: 627 sheet: 0.57 (1.03), residues: 24 loop : -1.07 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 79 TYR 0.009 0.001 TYR F 51 PHE 0.010 0.002 PHE D 65 TRP 0.010 0.001 TRP K 61 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 (14864) covalent geometry : angle 0.57743 / 0.34 (21353) hydrogen bonds : bond 0.06050 / 4.06 ( 813) hydrogen bonds : angle 3.25208 / 2.38 ( 2068) metal coordination : bond 0.00545 / 0.28 ( 8) metal coordination : angle 4.24147 / 2.18 ( 9) link_TRANS : bond 0.00047 / 0.02 ( 2) link_TRANS : angle 0.24491 / 0.12 ( 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 102 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.361 Fit side-chains REVERT: C 73 ASN cc_start: 0.7620 (m-40) cc_final: 0.6964 (t0) REVERT: D 99 ARG cc_start: 0.8289 (mtt-85) cc_final: 0.7734 (mtm-85) REVERT: H 47 GLN cc_start: 0.8462 (mt0) cc_final: 0.8242 (mt0) REVERT: H 99 ARG cc_start: 0.8327 (mtt-85) cc_final: 0.7637 (mtm180) REVERT: L 7 ASN cc_start: 0.8704 (m-40) cc_final: 0.8300 (m110) REVERT: L 8 LYS cc_start: 0.8437 (mmmm) cc_final: 0.8151 (mmtt) REVERT: L 30 MET cc_start: 0.5461 (mmm) cc_final: 0.5119 (mmm) REVERT: L 147 MET cc_start: 0.6689 (ptp) cc_final: 0.6388 (ptp) outliers start: 6 outliers final: 5 residues processed: 98 average time/residue: 0.1390 time to fit residues: 18.4399 Evaluate side-chains 94 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 75 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 23 optimal weight: 0.0870 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 119 optimal weight: 8.9990 chunk 106 optimal weight: 0.2980 chunk 112 optimal weight: 3.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN L 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.156208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.100589 restraints weight = 20717.164| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.48 r_work: 0.2736 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 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 = 0.2583 r_free = 0.2583 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: 0.2583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14874 Z= 0.135 Angle : 0.568 7.533 21368 Z= 0.331 Chirality : 0.042 0.228 2419 Planarity : 0.004 0.037 1688 Dihedral : 29.585 176.723 4332 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.58 % Allowed : 8.53 % Favored : 90.89 % 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: 2.08 (0.27), residues: 983 helix: 2.59 (0.21), residues: 626 sheet: 0.58 (1.03), residues: 24 loop : -1.01 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 17 TYR 0.009 0.001 TYR F 51 PHE 0.014 0.001 PHE L 50 TRP 0.008 0.001 TRP K 61 HIS 0.002 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.14 (14864) covalent geometry : angle 0.56171 / 0.33 (21353) hydrogen bonds : bond 0.05647 / 3.80 ( 813) hydrogen bonds : angle 3.19157 / 2.35 ( 2068) metal coordination : bond 0.00478 / 0.24 ( 8) metal coordination : angle 4.02650 / 2.09 ( 9) link_TRANS : bond 0.00056 / 0.03 ( 2) link_TRANS : angle 0.27900 / 0.14 ( 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 95 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.348 Fit side-chains REVERT: C 73 ASN cc_start: 0.7553 (m-40) cc_final: 0.6913 (t0) REVERT: D 99 ARG cc_start: 0.8343 (mtt-85) cc_final: 0.7775 (mtm-85) REVERT: H 47 GLN cc_start: 0.8497 (mt0) cc_final: 0.8245 (mt0) REVERT: H 99 ARG cc_start: 0.8413 (mtt-85) cc_final: 0.7676 (mtm180) REVERT: L 7 ASN cc_start: 0.8729 (m-40) cc_final: 0.8350 (m110) REVERT: L 8 LYS cc_start: 0.8389 (mmmm) cc_final: 0.8127 (mmtt) REVERT: L 30 MET cc_start: 0.5399 (mmm) cc_final: 0.5029 (mmm) REVERT: L 147 MET cc_start: 0.6774 (ptp) cc_final: 0.6503 (ptp) outliers start: 5 outliers final: 4 residues processed: 93 average time/residue: 0.1504 time to fit residues: 18.9187 Evaluate side-chains 91 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 17 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 118 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.156049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.100452 restraints weight = 29186.540| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.00 r_work: 0.2721 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 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 = 0.2660 r_free = 0.2660 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: 0.2660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14874 Z= 0.143 Angle : 0.563 7.362 21368 Z= 0.329 Chirality : 0.042 0.236 2419 Planarity : 0.004 0.036 1688 Dihedral : 29.591 176.319 4332 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.82 % Allowed : 8.88 % Favored : 90.30 % 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: 2.10 (0.27), residues: 983 helix: 2.59 (0.21), residues: 626 sheet: 0.61 (1.04), residues: 24 loop : -0.99 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 129 TYR 0.009 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 0.00266 / 0.14 (14864) covalent geometry : angle 0.55738 / 0.33 (21353) hydrogen bonds : bond 0.05607 / 3.78 ( 813) hydrogen bonds : angle 3.13800 / 2.30 ( 2068) metal coordination : bond 0.00497 / 0.26 ( 8) metal coordination : angle 4.02941 / 2.09 ( 9) link_TRANS : bond 0.00034 / 0.02 ( 2) link_TRANS : angle 0.27608 / 0.14 ( 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 99 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.346 Fit side-chains REVERT: C 73 ASN cc_start: 0.7522 (m-40) cc_final: 0.6894 (t0) REVERT: D 99 ARG cc_start: 0.8292 (mtt-85) cc_final: 0.7730 (mtm-85) REVERT: H 47 GLN cc_start: 0.8464 (mt0) cc_final: 0.8158 (mt0) REVERT: H 99 ARG cc_start: 0.8323 (mtt-85) cc_final: 0.7601 (mtm180) REVERT: L 7 ASN cc_start: 0.8730 (m-40) cc_final: 0.8304 (m110) REVERT: L 30 MET cc_start: 0.5342 (mmm) cc_final: 0.4948 (mmm) REVERT: L 147 MET cc_start: 0.6732 (ptp) cc_final: 0.6487 (ptp) outliers start: 7 outliers final: 5 residues processed: 96 average time/residue: 0.1403 time to fit residues: 18.4722 Evaluate side-chains 95 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 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: 0.0570 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: 0.7980 chunk 36 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.154604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.099753 restraints weight = 21059.711| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.58 r_work: 0.2695 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 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 = 0.2691 r_free = 0.2691 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: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14874 Z= 0.143 Angle : 0.560 7.500 21368 Z= 0.326 Chirality : 0.042 0.240 2419 Planarity : 0.004 0.037 1688 Dihedral : 29.661 176.415 4332 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.05 % Allowed : 8.88 % 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: 2.10 (0.27), residues: 983 helix: 2.59 (0.21), residues: 626 sheet: 0.62 (1.04), residues: 24 loop : -0.98 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 136 TYR 0.009 0.001 TYR F 51 PHE 0.016 0.002 PHE L 50 TRP 0.010 0.001 TRP K 61 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (14864) covalent geometry : angle 0.55403 / 0.33 (21353) hydrogen bonds : bond 0.05588 / 3.76 ( 813) hydrogen bonds : angle 3.06589 / 2.24 ( 2068) metal coordination : bond 0.00489 / 0.25 ( 8) metal coordination : angle 4.02711 / 2.08 ( 9) link_TRANS : bond 0.00023 / 0.01 ( 2) link_TRANS : angle 0.21595 / 0.11 ( 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 97 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.355 Fit side-chains REVERT: C 73 ASN cc_start: 0.7482 (m-40) cc_final: 0.6957 (t0) REVERT: D 99 ARG cc_start: 0.8274 (mtt-85) cc_final: 0.7745 (mtm-85) REVERT: H 47 GLN cc_start: 0.8597 (mt0) cc_final: 0.8308 (mt0) REVERT: H 99 ARG cc_start: 0.8297 (mtt-85) cc_final: 0.7631 (mtm180) REVERT: L 30 MET cc_start: 0.5437 (mmm) cc_final: 0.5039 (mmm) REVERT: L 147 MET cc_start: 0.6730 (ptp) cc_final: 0.6444 (ptp) outliers start: 9 outliers final: 7 residues processed: 92 average time/residue: 0.1545 time to fit residues: 19.2373 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 : 0.303 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 91 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 45 optimal weight: 0.0270 chunk 58 optimal weight: 1.9990 overall best weight: 1.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN L 92 GLN L 135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.153346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.098481 restraints weight = 20551.897| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.54 r_work: 0.2672 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 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 = 0.2662 r_free = 0.2662 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: 0.2662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14874 Z= 0.170 Angle : 0.592 8.099 21368 Z= 0.336 Chirality : 0.044 0.253 2419 Planarity : 0.004 0.036 1688 Dihedral : 29.810 176.441 4332 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.93 % Allowed : 9.23 % Favored : 89.84 % 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: 1.95 (0.27), residues: 983 helix: 2.48 (0.21), residues: 626 sheet: 0.55 (1.04), residues: 24 loop : -1.06 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 129 TYR 0.009 0.001 TYR F 51 PHE 0.018 0.002 PHE L 50 TRP 0.010 0.002 TRP K 61 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (14864) covalent geometry : angle 0.58577 / 0.34 (21353) hydrogen bonds : bond 0.06122 / 4.12 ( 813) hydrogen bonds : angle 3.16747 / 2.33 ( 2068) metal coordination : bond 0.00592 / 0.30 ( 8) metal coordination : angle 4.27982 / 2.19 ( 9) link_TRANS : bond 0.00069 / 0.04 ( 2) link_TRANS : angle 0.25754 / 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 98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.323 Fit side-chains REVERT: A 81 ASP cc_start: 0.7429 (t0) cc_final: 0.7185 (t0) REVERT: C 73 ASN cc_start: 0.7580 (m-40) cc_final: 0.7067 (t0) REVERT: D 99 ARG cc_start: 0.8271 (mtt-85) cc_final: 0.7845 (mtm-85) REVERT: H 99 ARG cc_start: 0.8312 (mtt-85) cc_final: 0.7941 (mtm-85) REVERT: L 7 ASN cc_start: 0.8846 (m110) cc_final: 0.8599 (m110) REVERT: L 30 MET cc_start: 0.5576 (mmm) cc_final: 0.5175 (mmm) REVERT: L 147 MET cc_start: 0.6748 (ptp) cc_final: 0.6480 (ptp) outliers start: 8 outliers final: 5 residues processed: 93 average time/residue: 0.1482 time to fit residues: 18.5254 Evaluate side-chains 95 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 60 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN L 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.155074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.099250 restraints weight = 26460.972| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.86 r_work: 0.2662 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 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 = 0.2654 r_free = 0.2654 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: 0.2654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1098 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= 0.130 Angle : 0.566 7.205 21368 Z= 0.326 Chirality : 0.043 0.224 2419 Planarity : 0.004 0.037 1688 Dihedral : 29.739 176.536 4332 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.82 % Allowed : 9.58 % Favored : 89.60 % 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: 2.08 (0.27), residues: 983 helix: 2.58 (0.21), residues: 626 sheet: 0.53 (1.03), residues: 24 loop : -1.01 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 129 TYR 0.008 0.001 TYR F 51 PHE 0.013 0.001 PHE L 50 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 0.00226 / 0.13 (14864) covalent geometry : angle 0.56038 / 0.33 (21353) hydrogen bonds : bond 0.05528 / 3.73 ( 813) hydrogen bonds : angle 3.07717 / 2.27 ( 2068) metal coordination : bond 0.00464 / 0.22 ( 8) metal coordination : angle 4.02488 / 2.10 ( 9) link_TRANS : bond 0.00065 / 0.03 ( 2) link_TRANS : angle 0.17991 / 0.09 ( 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 97 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.289 Fit side-chains REVERT: A 81 ASP cc_start: 0.7464 (t0) cc_final: 0.7200 (t0) REVERT: C 73 ASN cc_start: 0.7469 (m-40) cc_final: 0.6963 (t0) REVERT: D 99 ARG cc_start: 0.8295 (mtt-85) cc_final: 0.7778 (mtm-85) REVERT: H 99 ARG cc_start: 0.8303 (mtt-85) cc_final: 0.7549 (mtm180) REVERT: L 30 MET cc_start: 0.5480 (mmm) cc_final: 0.5078 (mmm) REVERT: L 147 MET cc_start: 0.6765 (ptp) cc_final: 0.6535 (ptp) outliers start: 7 outliers final: 5 residues processed: 93 average time/residue: 0.1544 time to fit residues: 19.3657 Evaluate side-chains 94 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 25 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 23 optimal weight: 0.0170 chunk 39 optimal weight: 0.5980 chunk 92 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 76 optimal weight: 10.0000 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN L 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.155636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.099554 restraints weight = 29067.300| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.99 r_work: 0.2704 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 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 = 0.2649 r_free = 0.2649 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: 0.2649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1108 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= 0.134 Angle : 0.555 7.131 21368 Z= 0.322 Chirality : 0.041 0.234 2419 Planarity : 0.004 0.037 1688 Dihedral : 29.694 176.531 4332 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.58 % Allowed : 10.16 % Favored : 89.25 % 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: 2.14 (0.27), residues: 983 helix: 2.62 (0.21), residues: 626 sheet: 0.52 (1.03), residues: 24 loop : -0.96 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 129 TYR 0.008 0.001 TYR F 51 PHE 0.012 0.001 PHE L 50 TRP 0.010 0.001 TRP K 61 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 (14864) covalent geometry : angle 0.54958 / 0.32 (21353) hydrogen bonds : bond 0.05349 / 3.61 ( 813) hydrogen bonds : angle 3.04246 / 2.26 ( 2068) metal coordination : bond 0.00491 / 0.24 ( 8) metal coordination : angle 3.99119 / 2.07 ( 9) link_TRANS : bond 0.00018 / 0.01 ( 2) link_TRANS : angle 0.21555 / 0.11 ( 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: 5 poor density : 89 time to evaluate : 0.277 Fit side-chains REVERT: A 81 ASP cc_start: 0.7471 (t0) cc_final: 0.7199 (t0) REVERT: C 73 ASN cc_start: 0.7289 (m-40) cc_final: 0.6852 (t0) REVERT: D 99 ARG cc_start: 0.8301 (mtt-85) cc_final: 0.7780 (mtm-85) REVERT: H 99 ARG cc_start: 0.8295 (mtt-85) cc_final: 0.7570 (mtm180) REVERT: L 30 MET cc_start: 0.5515 (mmm) cc_final: 0.5114 (mmm) REVERT: L 147 MET cc_start: 0.6750 (ptp) cc_final: 0.6506 (ptp) outliers start: 5 outliers final: 4 residues processed: 91 average time/residue: 0.1492 time to fit residues: 18.3376 Evaluate side-chains 91 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 101 optimal weight: 0.0020 chunk 119 optimal weight: 0.7980 chunk 43 optimal weight: 0.3980 chunk 114 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 72 optimal weight: 30.0000 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN H 47 GLN L 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.157515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.102230 restraints weight = 26954.622| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.88 r_work: 0.2727 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 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 = 0.2692 r_free = 0.2692 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: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1114 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= 0.127 Angle : 0.552 8.696 21368 Z= 0.321 Chirality : 0.041 0.227 2419 Planarity : 0.004 0.038 1688 Dihedral : 29.671 176.717 4332 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.58 % Allowed : 10.28 % Favored : 89.14 % 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: 2.18 (0.27), residues: 983 helix: 2.65 (0.21), residues: 626 sheet: 0.54 (1.03), residues: 24 loop : -0.94 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 116 TYR 0.008 0.001 TYR F 51 PHE 0.011 0.001 PHE L 50 TRP 0.009 0.001 TRP K 61 HIS 0.002 0.000 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.13 (14864) covalent geometry : angle 0.54595 / 0.32 (21353) hydrogen bonds : bond 0.05223 / 3.52 ( 813) hydrogen bonds : angle 3.05570 / 2.30 ( 2068) metal coordination : bond 0.00483 / 0.23 ( 8) metal coordination : angle 3.90276 / 2.03 ( 9) link_TRANS : bond 0.00047 / 0.02 ( 2) link_TRANS : angle 0.20438 / 0.10 ( 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 93 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.299 Fit side-chains REVERT: A 81 ASP cc_start: 0.7447 (t0) cc_final: 0.7171 (t0) REVERT: C 73 ASN cc_start: 0.7290 (m-40) cc_final: 0.6875 (t0) REVERT: D 99 ARG cc_start: 0.8290 (mtt-85) cc_final: 0.7789 (mtm-85) REVERT: H 99 ARG cc_start: 0.8297 (mtt-85) cc_final: 0.7537 (mtm180) REVERT: L 7 ASN cc_start: 0.8735 (m110) cc_final: 0.8481 (m110) REVERT: L 30 MET cc_start: 0.5548 (mmm) cc_final: 0.5155 (mmm) REVERT: L 147 MET cc_start: 0.6746 (ptp) cc_final: 0.6485 (ptp) outliers start: 5 outliers final: 5 residues processed: 89 average time/residue: 0.1510 time to fit residues: 18.1132 Evaluate side-chains 92 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 109 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN L 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.149490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.108897 restraints weight = 21074.010| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.57 r_work: 0.2680 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1146 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= 0.142 Angle : 0.560 8.675 21368 Z= 0.324 Chirality : 0.042 0.239 2419 Planarity : 0.004 0.037 1688 Dihedral : 29.711 176.582 4332 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.58 % Allowed : 10.63 % Favored : 88.79 % 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: 2.60 (0.21), residues: 626 sheet: 0.52 (1.03), residues: 24 loop : -0.98 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 136 TYR 0.008 0.001 TYR F 51 PHE 0.012 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 0.00271 / 0.14 (14864) covalent geometry : angle 0.55433 / 0.32 (21353) hydrogen bonds : bond 0.05430 / 3.65 ( 813) hydrogen bonds : angle 3.06564 / 2.29 ( 2068) metal coordination : bond 0.00470 / 0.24 ( 8) metal coordination : angle 4.00718 / 2.07 ( 9) link_TRANS : bond 0.00037 / 0.02 ( 2) link_TRANS : angle 0.21044 / 0.11 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2871.66 seconds wall clock time: 49 minutes 43.13 seconds (2983.13 seconds total)