Starting phenix.real_space_refine on Wed Feb 4 11:22:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h1p_51769/02_2026/9h1p_51769.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h1p_51769/02_2026/9h1p_51769.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9h1p_51769/02_2026/9h1p_51769.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h1p_51769/02_2026/9h1p_51769.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9h1p_51769/02_2026/9h1p_51769.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h1p_51769/02_2026/9h1p_51769.map" } resolution = 3.1 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= -0.004 sd= 0.040 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 6696 2.51 5 N 1932 2.21 5 O 2016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10668 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 834 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain: "B" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5} Restraints were copied for chains: C, E, G, I, K, M, O, Q, S, U, W, D, F, H, J, L, N, P, R, T, V, X Time building chain proxies: 0.93, per 1000 atoms: 0.09 Number of scatterers: 10668 At special positions: 0 Unit cell: (167.2, 165.3, 50.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 2016 8.00 N 1932 7.00 C 6696 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 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 484.8 milliseconds 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 0 sheets defined 68.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 9 through 17 Processing helix chain 'A' and resid 30 through 42 removed outlier: 3.893A pdb=" N ILE A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 72 through 90 Processing helix chain 'A' and resid 96 through 108 removed outlier: 3.799A pdb=" N GLU A 107 " --> pdb=" O LYS A 103 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 17 Processing helix chain 'C' and resid 30 through 42 removed outlier: 3.893A pdb=" N ILE C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 Processing helix chain 'C' and resid 53 through 65 Processing helix chain 'C' and resid 66 through 68 No H-bonds generated for 'chain 'C' and resid 66 through 68' Processing helix chain 'C' and resid 72 through 90 Processing helix chain 'C' and resid 96 through 108 removed outlier: 3.799A pdb=" N GLU C 107 " --> pdb=" O LYS C 103 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN C 108 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 17 Processing helix chain 'E' and resid 30 through 42 removed outlier: 3.893A pdb=" N ILE E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU E 42 " --> pdb=" O SER E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 Processing helix chain 'E' and resid 53 through 65 Processing helix chain 'E' and resid 66 through 68 No H-bonds generated for 'chain 'E' and resid 66 through 68' Processing helix chain 'E' and resid 72 through 90 Processing helix chain 'E' and resid 96 through 108 removed outlier: 3.798A pdb=" N GLU E 107 " --> pdb=" O LYS E 103 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN E 108 " --> pdb=" O ILE E 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 17 Processing helix chain 'G' and resid 30 through 42 removed outlier: 3.893A pdb=" N ILE G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU G 42 " --> pdb=" O SER G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 52 Processing helix chain 'G' and resid 53 through 65 Processing helix chain 'G' and resid 66 through 68 No H-bonds generated for 'chain 'G' and resid 66 through 68' Processing helix chain 'G' and resid 72 through 90 Processing helix chain 'G' and resid 96 through 108 removed outlier: 3.799A pdb=" N GLU G 107 " --> pdb=" O LYS G 103 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN G 108 " --> pdb=" O ILE G 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 17 Processing helix chain 'I' and resid 30 through 42 removed outlier: 3.893A pdb=" N ILE I 34 " --> pdb=" O LYS I 30 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU I 42 " --> pdb=" O SER I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 52 Processing helix chain 'I' and resid 53 through 65 Processing helix chain 'I' and resid 66 through 68 No H-bonds generated for 'chain 'I' and resid 66 through 68' Processing helix chain 'I' and resid 72 through 90 Processing helix chain 'I' and resid 96 through 108 removed outlier: 3.798A pdb=" N GLU I 107 " --> pdb=" O LYS I 103 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN I 108 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 17 Processing helix chain 'K' and resid 30 through 42 removed outlier: 3.894A pdb=" N ILE K 34 " --> pdb=" O LYS K 30 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU K 42 " --> pdb=" O SER K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 52 Processing helix chain 'K' and resid 53 through 65 Processing helix chain 'K' and resid 66 through 68 No H-bonds generated for 'chain 'K' and resid 66 through 68' Processing helix chain 'K' and resid 72 through 90 Processing helix chain 'K' and resid 96 through 108 removed outlier: 3.799A pdb=" N GLU K 107 " --> pdb=" O LYS K 103 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN K 108 " --> pdb=" O ILE K 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 17 Processing helix chain 'M' and resid 30 through 42 removed outlier: 3.894A pdb=" N ILE M 34 " --> pdb=" O LYS M 30 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 52 Processing helix chain 'M' and resid 53 through 65 Processing helix chain 'M' and resid 66 through 68 No H-bonds generated for 'chain 'M' and resid 66 through 68' Processing helix chain 'M' and resid 72 through 90 Processing helix chain 'M' and resid 96 through 108 removed outlier: 3.798A pdb=" N GLU M 107 " --> pdb=" O LYS M 103 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN M 108 " --> pdb=" O ILE M 104 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 17 Processing helix chain 'O' and resid 30 through 42 removed outlier: 3.893A pdb=" N ILE O 34 " --> pdb=" O LYS O 30 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU O 42 " --> pdb=" O SER O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 47 through 52 Processing helix chain 'O' and resid 53 through 65 Processing helix chain 'O' and resid 66 through 68 No H-bonds generated for 'chain 'O' and resid 66 through 68' Processing helix chain 'O' and resid 72 through 90 Processing helix chain 'O' and resid 96 through 108 removed outlier: 3.799A pdb=" N GLU O 107 " --> pdb=" O LYS O 103 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN O 108 " --> pdb=" O ILE O 104 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 17 Processing helix chain 'Q' and resid 30 through 42 removed outlier: 3.892A pdb=" N ILE Q 34 " --> pdb=" O LYS Q 30 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU Q 42 " --> pdb=" O SER Q 38 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 52 Processing helix chain 'Q' and resid 53 through 65 Processing helix chain 'Q' and resid 66 through 68 No H-bonds generated for 'chain 'Q' and resid 66 through 68' Processing helix chain 'Q' and resid 72 through 90 Processing helix chain 'Q' and resid 96 through 108 removed outlier: 3.799A pdb=" N GLU Q 107 " --> pdb=" O LYS Q 103 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN Q 108 " --> pdb=" O ILE Q 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 17 Processing helix chain 'S' and resid 30 through 42 removed outlier: 3.892A pdb=" N ILE S 34 " --> pdb=" O LYS S 30 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU S 42 " --> pdb=" O SER S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 47 through 52 Processing helix chain 'S' and resid 53 through 65 Processing helix chain 'S' and resid 66 through 68 No H-bonds generated for 'chain 'S' and resid 66 through 68' Processing helix chain 'S' and resid 72 through 90 Processing helix chain 'S' and resid 96 through 108 removed outlier: 3.799A pdb=" N GLU S 107 " --> pdb=" O LYS S 103 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN S 108 " --> pdb=" O ILE S 104 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 17 Processing helix chain 'U' and resid 30 through 42 removed outlier: 3.893A pdb=" N ILE U 34 " --> pdb=" O LYS U 30 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU U 42 " --> pdb=" O SER U 38 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 52 Processing helix chain 'U' and resid 53 through 65 Processing helix chain 'U' and resid 66 through 68 No H-bonds generated for 'chain 'U' and resid 66 through 68' Processing helix chain 'U' and resid 72 through 90 Processing helix chain 'U' and resid 96 through 108 removed outlier: 3.798A pdb=" N GLU U 107 " --> pdb=" O LYS U 103 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN U 108 " --> pdb=" O ILE U 104 " (cutoff:3.500A) Processing helix chain 'W' and resid 9 through 17 Processing helix chain 'W' and resid 30 through 42 removed outlier: 3.894A pdb=" N ILE W 34 " --> pdb=" O LYS W 30 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU W 42 " --> pdb=" O SER W 38 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 52 Processing helix chain 'W' and resid 53 through 65 Processing helix chain 'W' and resid 66 through 68 No H-bonds generated for 'chain 'W' and resid 66 through 68' Processing helix chain 'W' and resid 72 through 90 Processing helix chain 'W' and resid 96 through 108 removed outlier: 3.797A pdb=" N GLU W 107 " --> pdb=" O LYS W 103 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN W 108 " --> pdb=" O ILE W 104 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1548 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.18 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3612 1.34 - 1.46: 1426 1.46 - 1.57: 5762 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 10824 Sorted by residual: bond pdb=" CB THR U 97 " pdb=" CG2 THR U 97 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.81e-01 bond pdb=" CB THR M 97 " pdb=" CG2 THR M 97 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.80e-01 bond pdb=" CB THR I 97 " pdb=" CG2 THR I 97 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.72e-01 bond pdb=" CB THR O 97 " pdb=" CG2 THR O 97 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.68e-01 bond pdb=" CB THR A 97 " pdb=" CG2 THR A 97 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.67e-01 ... (remaining 10819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 12774 0.94 - 1.88: 1386 1.88 - 2.82: 288 2.82 - 3.76: 60 3.76 - 4.70: 12 Bond angle restraints: 14520 Sorted by residual: angle pdb=" C LYS I 15 " pdb=" N TRP I 16 " pdb=" CA TRP I 16 " ideal model delta sigma weight residual 120.44 123.94 -3.50 1.30e+00 5.92e-01 7.26e+00 angle pdb=" C LYS E 15 " pdb=" N TRP E 16 " pdb=" CA TRP E 16 " ideal model delta sigma weight residual 120.44 123.93 -3.49 1.30e+00 5.92e-01 7.20e+00 angle pdb=" C LYS A 15 " pdb=" N TRP A 16 " pdb=" CA TRP A 16 " ideal model delta sigma weight residual 120.44 123.92 -3.48 1.30e+00 5.92e-01 7.17e+00 angle pdb=" C LYS C 15 " pdb=" N TRP C 16 " pdb=" CA TRP C 16 " ideal model delta sigma weight residual 120.44 123.91 -3.47 1.30e+00 5.92e-01 7.13e+00 angle pdb=" C LYS S 15 " pdb=" N TRP S 16 " pdb=" CA TRP S 16 " ideal model delta sigma weight residual 120.44 123.91 -3.47 1.30e+00 5.92e-01 7.11e+00 ... (remaining 14515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.44: 5940 14.44 - 28.88: 468 28.88 - 43.31: 156 43.31 - 57.75: 48 57.75 - 72.19: 48 Dihedral angle restraints: 6660 sinusoidal: 2892 harmonic: 3768 Sorted by residual: dihedral pdb=" CA GLN K 28 " pdb=" C GLN K 28 " pdb=" N TYR K 29 " pdb=" CA TYR K 29 " ideal model delta harmonic sigma weight residual 180.00 159.43 20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA GLN O 28 " pdb=" C GLN O 28 " pdb=" N TYR O 29 " pdb=" CA TYR O 29 " ideal model delta harmonic sigma weight residual 180.00 159.45 20.55 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA GLN G 28 " pdb=" C GLN G 28 " pdb=" N TYR G 29 " pdb=" CA TYR G 29 " ideal model delta harmonic sigma weight residual 180.00 159.47 20.53 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 6657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 628 0.024 - 0.048: 540 0.048 - 0.071: 205 0.071 - 0.095: 116 0.095 - 0.119: 83 Chirality restraints: 1572 Sorted by residual: chirality pdb=" CA PRO K 66 " pdb=" N PRO K 66 " pdb=" C PRO K 66 " pdb=" CB PRO K 66 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.53e-01 chirality pdb=" CA PRO A 66 " pdb=" N PRO A 66 " pdb=" C PRO A 66 " pdb=" CB PRO A 66 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA PRO O 66 " pdb=" N PRO O 66 " pdb=" C PRO O 66 " pdb=" CB PRO O 66 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.49e-01 ... (remaining 1569 not shown) Planarity restraints: 1884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 12 " -0.210 9.50e-02 1.11e+02 9.51e-02 7.58e+00 pdb=" NE ARG J 12 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG J 12 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG J 12 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG J 12 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 12 " 0.210 9.50e-02 1.11e+02 9.51e-02 7.51e+00 pdb=" NE ARG N 12 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG N 12 " 0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG N 12 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG N 12 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 12 " 0.210 9.50e-02 1.11e+02 9.50e-02 7.50e+00 pdb=" NE ARG H 12 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG H 12 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG H 12 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG H 12 " -0.001 2.00e-02 2.50e+03 ... (remaining 1881 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 4474 2.97 - 3.45: 10998 3.45 - 3.93: 16909 3.93 - 4.42: 19702 4.42 - 4.90: 30912 Nonbonded interactions: 82995 Sorted by model distance: nonbonded pdb=" OE2 GLU G 42 " pdb=" NH1 ARG G 43 " model vdw 2.482 3.120 nonbonded pdb=" OE2 GLU W 42 " pdb=" NH1 ARG W 43 " model vdw 2.482 3.120 nonbonded pdb=" OE2 GLU K 42 " pdb=" NH1 ARG K 43 " model vdw 2.482 3.120 nonbonded pdb=" OE2 GLU O 42 " pdb=" NH1 ARG O 43 " model vdw 2.482 3.120 nonbonded pdb=" OE2 GLU I 42 " pdb=" NH1 ARG I 43 " model vdw 2.482 3.120 ... (remaining 82990 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 12.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.040 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 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 : 0.004 0.026 10824 Z= 0.171 Angle : 0.669 4.701 14520 Z= 0.402 Chirality : 0.045 0.119 1572 Planarity : 0.010 0.095 1884 Dihedral : 13.913 72.187 4236 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.20), residues: 1284 helix: -0.46 (0.17), residues: 840 sheet: None (None), residues: 0 loop : -0.77 (0.19), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.003 ARG J 12 TYR 0.011 0.003 TYR E 29 PHE 0.013 0.003 PHE N 16 TRP 0.023 0.004 TRP K 16 HIS 0.003 0.001 HIS W 89 Details of bonding type rmsd covalent geometry : bond 0.00364 (10824) covalent geometry : angle 0.66885 (14520) hydrogen bonds : bond 0.11971 ( 552) hydrogen bonds : angle 3.88040 ( 1548) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.376 Fit side-chains REVERT: A 27 LYS cc_start: 0.8018 (mttt) cc_final: 0.7789 (mttt) REVERT: A 39 ARG cc_start: 0.7729 (ttm-80) cc_final: 0.7461 (ttm-80) REVERT: A 40 GLU cc_start: 0.7812 (tp30) cc_final: 0.7612 (tp30) REVERT: A 43 ARG cc_start: 0.6826 (mmt-90) cc_final: 0.5691 (ptm-80) REVERT: A 52 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8071 (mt-10) REVERT: C 43 ARG cc_start: 0.6795 (mmt-90) cc_final: 0.5806 (ptm-80) REVERT: E 40 GLU cc_start: 0.7741 (tp30) cc_final: 0.7533 (tp30) REVERT: E 43 ARG cc_start: 0.6884 (mmt-90) cc_final: 0.5719 (ptm-80) REVERT: G 43 ARG cc_start: 0.6870 (mmt-90) cc_final: 0.5896 (ttp-170) REVERT: I 39 ARG cc_start: 0.7790 (ttm-80) cc_final: 0.7444 (tmm160) REVERT: I 43 ARG cc_start: 0.6996 (mmt-90) cc_final: 0.6346 (ttp80) REVERT: I 52 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7833 (mt-10) REVERT: K 39 ARG cc_start: 0.7459 (ttm-80) cc_final: 0.7155 (ttm170) REVERT: K 43 ARG cc_start: 0.6765 (mmt-90) cc_final: 0.6166 (ttp80) REVERT: M 43 ARG cc_start: 0.6991 (mmt-90) cc_final: 0.6382 (ttp80) REVERT: M 90 GLN cc_start: 0.7385 (tp40) cc_final: 0.7184 (mm-40) REVERT: O 39 ARG cc_start: 0.7603 (ttm-80) cc_final: 0.7294 (ttp-170) REVERT: O 43 ARG cc_start: 0.6993 (mmt-90) cc_final: 0.6537 (mtp-110) REVERT: Q 40 GLU cc_start: 0.7567 (tp30) cc_final: 0.7349 (tp30) REVERT: Q 43 ARG cc_start: 0.6960 (mmt-90) cc_final: 0.6075 (ttp80) REVERT: S 39 ARG cc_start: 0.7506 (ttm-80) cc_final: 0.7120 (ttp-170) REVERT: S 43 ARG cc_start: 0.6756 (mmt-90) cc_final: 0.6064 (ttp80) REVERT: S 52 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8071 (mt-10) REVERT: S 63 GLN cc_start: 0.8029 (tp40) cc_final: 0.7822 (tp40) REVERT: U 40 GLU cc_start: 0.7517 (tp30) cc_final: 0.7262 (tp30) REVERT: U 43 ARG cc_start: 0.6980 (mmt-90) cc_final: 0.5978 (ttp80) REVERT: W 39 ARG cc_start: 0.7824 (ttm-80) cc_final: 0.7488 (tmm160) REVERT: W 43 ARG cc_start: 0.6829 (mmt-90) cc_final: 0.6125 (ttp80) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1490 time to fit residues: 31.9563 Evaluate side-chains 149 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN K 59 GLN K 90 GLN S 59 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.163693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.126137 restraints weight = 9979.551| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.51 r_work: 0.3266 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10824 Z= 0.132 Angle : 0.476 4.624 14520 Z= 0.256 Chirality : 0.038 0.117 1572 Planarity : 0.004 0.035 1884 Dihedral : 4.284 13.249 1452 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.17 % Allowed : 3.65 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.21), residues: 1284 helix: 1.23 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -1.19 (0.19), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 39 TYR 0.013 0.001 TYR A 29 PHE 0.010 0.001 PHE B 16 TRP 0.014 0.002 TRP U 16 HIS 0.003 0.001 HIS Q 89 Details of bonding type rmsd covalent geometry : bond 0.00318 (10824) covalent geometry : angle 0.47620 (14520) hydrogen bonds : bond 0.04626 ( 552) hydrogen bonds : angle 3.24313 ( 1548) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 0.444 Fit side-chains REVERT: A 43 ARG cc_start: 0.7077 (mmt-90) cc_final: 0.5482 (ptm-80) REVERT: C 43 ARG cc_start: 0.7059 (mmt-90) cc_final: 0.5564 (ptm-80) REVERT: E 40 GLU cc_start: 0.7501 (tp30) cc_final: 0.6995 (tp30) REVERT: E 43 ARG cc_start: 0.7065 (mmt-90) cc_final: 0.5355 (ptm-80) REVERT: G 43 ARG cc_start: 0.7020 (mmt-90) cc_final: 0.5673 (ttp-170) REVERT: I 39 ARG cc_start: 0.7425 (ttm-80) cc_final: 0.7022 (ttp-170) REVERT: I 43 ARG cc_start: 0.7194 (mmt-90) cc_final: 0.5572 (ptm160) REVERT: K 39 ARG cc_start: 0.7170 (ttm-80) cc_final: 0.6811 (ttp-170) REVERT: K 43 ARG cc_start: 0.7188 (mmt-90) cc_final: 0.6047 (mtp-110) REVERT: M 43 ARG cc_start: 0.7138 (mmt-90) cc_final: 0.5860 (ttp80) REVERT: O 39 ARG cc_start: 0.7394 (ttm-80) cc_final: 0.6968 (ttp-170) REVERT: O 43 ARG cc_start: 0.7384 (mmt-90) cc_final: 0.6265 (mtp-110) REVERT: Q 40 GLU cc_start: 0.7383 (tp30) cc_final: 0.7146 (tp30) REVERT: Q 43 ARG cc_start: 0.7105 (mmt-90) cc_final: 0.5312 (ptm-80) REVERT: Q 90 GLN cc_start: 0.6813 (mm110) cc_final: 0.6552 (mm110) REVERT: S 39 ARG cc_start: 0.7185 (ttm-80) cc_final: 0.6751 (ttm170) REVERT: S 43 ARG cc_start: 0.7148 (mmt-90) cc_final: 0.5899 (ttp80) REVERT: S 52 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7522 (mt-10) REVERT: S 63 GLN cc_start: 0.7693 (tp40) cc_final: 0.7425 (tp40) REVERT: U 43 ARG cc_start: 0.7131 (mmt-90) cc_final: 0.5581 (ttp80) REVERT: W 28 GLN cc_start: 0.8160 (mm110) cc_final: 0.7738 (mm110) REVERT: W 39 ARG cc_start: 0.7463 (ttm-80) cc_final: 0.6974 (tmm160) REVERT: W 43 ARG cc_start: 0.6898 (mmt-90) cc_final: 0.5680 (ttp80) outliers start: 2 outliers final: 1 residues processed: 155 average time/residue: 0.2085 time to fit residues: 39.5688 Evaluate side-chains 145 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 20 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 113 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 115 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 0.0000 chunk 35 optimal weight: 2.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN J 15 ASN K 59 GLN S 59 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.163581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.126006 restraints weight = 10039.209| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.52 r_work: 0.3250 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10824 Z= 0.097 Angle : 0.395 4.562 14520 Z= 0.211 Chirality : 0.036 0.117 1572 Planarity : 0.004 0.025 1884 Dihedral : 3.564 11.306 1452 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 0.52 % Allowed : 4.95 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.23), residues: 1284 helix: 1.79 (0.19), residues: 852 sheet: None (None), residues: 0 loop : -1.34 (0.19), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 39 TYR 0.006 0.001 TYR A 29 PHE 0.004 0.001 PHE T 16 TRP 0.012 0.002 TRP E 16 HIS 0.002 0.001 HIS C 89 Details of bonding type rmsd covalent geometry : bond 0.00224 (10824) covalent geometry : angle 0.39459 (14520) hydrogen bonds : bond 0.03605 ( 552) hydrogen bonds : angle 2.97943 ( 1548) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 158 time to evaluate : 0.431 Fit side-chains REVERT: A 40 GLU cc_start: 0.7794 (tp30) cc_final: 0.7561 (tp30) REVERT: A 43 ARG cc_start: 0.7002 (mmt-90) cc_final: 0.5317 (ptm-80) REVERT: C 43 ARG cc_start: 0.7041 (mmt-90) cc_final: 0.5523 (ptm-80) REVERT: E 39 ARG cc_start: 0.7570 (ttm-80) cc_final: 0.7288 (ttm110) REVERT: E 40 GLU cc_start: 0.7498 (tp30) cc_final: 0.7092 (tp30) REVERT: E 43 ARG cc_start: 0.7060 (mmt-90) cc_final: 0.5423 (ptm-80) REVERT: G 43 ARG cc_start: 0.6976 (mmt-90) cc_final: 0.5483 (ttp-170) REVERT: I 39 ARG cc_start: 0.7514 (ttm-80) cc_final: 0.7166 (ttp-170) REVERT: I 43 ARG cc_start: 0.7119 (mmt-90) cc_final: 0.5490 (ptm160) REVERT: K 39 ARG cc_start: 0.7284 (ttm-80) cc_final: 0.6874 (ttp-170) REVERT: K 43 ARG cc_start: 0.7091 (mmt-90) cc_final: 0.5764 (ttp80) REVERT: M 43 ARG cc_start: 0.7091 (mmt-90) cc_final: 0.5817 (ttp80) REVERT: O 39 ARG cc_start: 0.7561 (ttm-80) cc_final: 0.7088 (ttp-170) REVERT: O 43 ARG cc_start: 0.7264 (mmt-90) cc_final: 0.6068 (mtp-110) REVERT: Q 43 ARG cc_start: 0.7069 (mmt-90) cc_final: 0.5251 (ptm-80) REVERT: Q 90 GLN cc_start: 0.6932 (mm110) cc_final: 0.6668 (mm110) REVERT: S 39 ARG cc_start: 0.7340 (ttm-80) cc_final: 0.6871 (ttm170) REVERT: S 43 ARG cc_start: 0.7185 (mmt-90) cc_final: 0.5844 (ttp80) REVERT: U 43 ARG cc_start: 0.7102 (mmt-90) cc_final: 0.5569 (ttp80) REVERT: W 28 GLN cc_start: 0.8054 (mm110) cc_final: 0.7619 (mm-40) REVERT: W 39 ARG cc_start: 0.7468 (ttm-80) cc_final: 0.6960 (ttp-170) REVERT: W 43 ARG cc_start: 0.6874 (mmt-90) cc_final: 0.5650 (ttp80) REVERT: W 105 GLU cc_start: 0.7275 (tt0) cc_final: 0.7030 (tt0) outliers start: 6 outliers final: 1 residues processed: 160 average time/residue: 0.1896 time to fit residues: 37.5827 Evaluate side-chains 148 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 20 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 82 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 59 GLN S 28 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.158251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.120044 restraints weight = 10153.627| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.59 r_work: 0.3198 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10824 Z= 0.143 Angle : 0.446 4.628 14520 Z= 0.234 Chirality : 0.037 0.120 1572 Planarity : 0.004 0.027 1884 Dihedral : 3.738 13.395 1452 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.87 % Allowed : 5.99 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.23), residues: 1284 helix: 1.88 (0.19), residues: 852 sheet: None (None), residues: 0 loop : -1.62 (0.18), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 39 TYR 0.007 0.001 TYR A 29 PHE 0.007 0.001 PHE D 16 TRP 0.012 0.002 TRP W 16 HIS 0.002 0.001 HIS G 33 Details of bonding type rmsd covalent geometry : bond 0.00359 (10824) covalent geometry : angle 0.44601 (14520) hydrogen bonds : bond 0.04396 ( 552) hydrogen bonds : angle 3.13224 ( 1548) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.431 Fit side-chains REVERT: C 43 ARG cc_start: 0.7341 (mmt-90) cc_final: 0.5753 (ptm-80) REVERT: E 39 ARG cc_start: 0.7697 (ttm-80) cc_final: 0.7444 (ttm110) REVERT: E 40 GLU cc_start: 0.7602 (tp30) cc_final: 0.7214 (tp30) REVERT: E 43 ARG cc_start: 0.7250 (mmt-90) cc_final: 0.5444 (ptm-80) REVERT: E 105 GLU cc_start: 0.7164 (tt0) cc_final: 0.6960 (tt0) REVERT: G 90 GLN cc_start: 0.6970 (mm110) cc_final: 0.6670 (mm110) REVERT: I 39 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.7120 (ttp-170) REVERT: K 39 ARG cc_start: 0.7476 (ttm-80) cc_final: 0.6999 (ttm170) REVERT: K 43 ARG cc_start: 0.7218 (mmt-90) cc_final: 0.6068 (mtp-110) REVERT: M 43 ARG cc_start: 0.7196 (mmt-90) cc_final: 0.5699 (ptm160) REVERT: O 39 ARG cc_start: 0.7733 (ttm-80) cc_final: 0.7265 (ttp-170) REVERT: O 43 ARG cc_start: 0.7355 (mmt-90) cc_final: 0.6117 (mtp-110) REVERT: Q 90 GLN cc_start: 0.7091 (mm110) cc_final: 0.6830 (mm110) REVERT: S 39 ARG cc_start: 0.7417 (ttm-80) cc_final: 0.6888 (ttm170) REVERT: S 43 ARG cc_start: 0.7362 (mmt-90) cc_final: 0.6100 (ttp80) REVERT: W 28 GLN cc_start: 0.8218 (mm110) cc_final: 0.7786 (mm-40) REVERT: W 39 ARG cc_start: 0.7445 (ttm-80) cc_final: 0.6844 (tmm160) REVERT: W 105 GLU cc_start: 0.7262 (tt0) cc_final: 0.6995 (tt0) outliers start: 10 outliers final: 6 residues processed: 142 average time/residue: 0.1875 time to fit residues: 33.2793 Evaluate side-chains 145 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain Q residue 20 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 38 optimal weight: 0.0570 chunk 79 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 59 GLN ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN O 59 GLN S 28 GLN S 59 GLN ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.160246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.122914 restraints weight = 10041.874| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.50 r_work: 0.3222 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10824 Z= 0.098 Angle : 0.381 4.520 14520 Z= 0.201 Chirality : 0.036 0.116 1572 Planarity : 0.003 0.025 1884 Dihedral : 3.345 10.227 1452 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.22 % Allowed : 6.16 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.23), residues: 1284 helix: 2.08 (0.19), residues: 852 sheet: None (None), residues: 0 loop : -1.56 (0.19), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 39 TYR 0.005 0.001 TYR A 29 PHE 0.003 0.001 PHE F 16 TRP 0.012 0.002 TRP C 16 HIS 0.001 0.001 HIS C 89 Details of bonding type rmsd covalent geometry : bond 0.00236 (10824) covalent geometry : angle 0.38148 (14520) hydrogen bonds : bond 0.03493 ( 552) hydrogen bonds : angle 2.94502 ( 1548) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.378 Fit side-chains REVERT: A 43 ARG cc_start: 0.7075 (mmt-90) cc_final: 0.5366 (ptm-80) REVERT: C 43 ARG cc_start: 0.7179 (mmt-90) cc_final: 0.5528 (ptm-80) REVERT: E 39 ARG cc_start: 0.7731 (ttm-80) cc_final: 0.7474 (ttm110) REVERT: E 40 GLU cc_start: 0.7614 (tp30) cc_final: 0.7261 (tp30) REVERT: E 43 ARG cc_start: 0.7137 (mmt-90) cc_final: 0.5379 (ptm-80) REVERT: I 39 ARG cc_start: 0.7562 (ttm-80) cc_final: 0.7191 (ttp-170) REVERT: I 43 ARG cc_start: 0.7120 (mmt-90) cc_final: 0.5392 (ptm160) REVERT: K 39 ARG cc_start: 0.7478 (ttm-80) cc_final: 0.7008 (ttm170) REVERT: K 43 ARG cc_start: 0.7142 (mmt-90) cc_final: 0.5949 (mtp-110) REVERT: M 43 ARG cc_start: 0.7110 (mmt-90) cc_final: 0.5652 (ptm160) REVERT: O 39 ARG cc_start: 0.7771 (ttm-80) cc_final: 0.7280 (ttp-170) REVERT: O 43 ARG cc_start: 0.7326 (mmt-90) cc_final: 0.6073 (mtp-110) REVERT: S 39 ARG cc_start: 0.7477 (ttm-80) cc_final: 0.6910 (ttm170) REVERT: S 43 ARG cc_start: 0.7299 (mmt-90) cc_final: 0.6005 (ttp80) REVERT: T 12 ARG cc_start: 0.8256 (ptm-80) cc_final: 0.8036 (ptm-80) REVERT: U 43 ARG cc_start: 0.7101 (mmt-90) cc_final: 0.5470 (ttp80) REVERT: W 28 GLN cc_start: 0.8188 (mm110) cc_final: 0.7845 (mm-40) REVERT: W 39 ARG cc_start: 0.7482 (ttm-80) cc_final: 0.6898 (tmm160) REVERT: W 105 GLU cc_start: 0.7284 (tt0) cc_final: 0.7009 (tt0) outliers start: 14 outliers final: 11 residues processed: 152 average time/residue: 0.1865 time to fit residues: 35.2989 Evaluate side-chains 159 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain M residue 95 LYS Chi-restraints excluded: chain Q residue 20 ARG Chi-restraints excluded: chain Q residue 95 LYS Chi-restraints excluded: chain W residue 50 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 112 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 86 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 72 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 59 GLN ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN S 59 GLN S 80 ASN ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.163946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.127774 restraints weight = 9905.156| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.45 r_work: 0.3212 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10824 Z= 0.106 Angle : 0.392 5.188 14520 Z= 0.205 Chirality : 0.036 0.115 1572 Planarity : 0.003 0.031 1884 Dihedral : 3.324 9.685 1452 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.39 % Allowed : 7.38 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.23), residues: 1284 helix: 2.25 (0.19), residues: 840 sheet: None (None), residues: 0 loop : -1.65 (0.19), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 39 TYR 0.005 0.001 TYR E 79 PHE 0.004 0.001 PHE D 16 TRP 0.012 0.001 TRP W 16 HIS 0.002 0.001 HIS C 89 Details of bonding type rmsd covalent geometry : bond 0.00258 (10824) covalent geometry : angle 0.39246 (14520) hydrogen bonds : bond 0.03673 ( 552) hydrogen bonds : angle 2.95208 ( 1548) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.435 Fit side-chains REVERT: C 43 ARG cc_start: 0.7274 (mmt-90) cc_final: 0.5635 (ptm-80) REVERT: E 39 ARG cc_start: 0.7732 (ttm-80) cc_final: 0.7469 (ttm110) REVERT: E 40 GLU cc_start: 0.7628 (tp30) cc_final: 0.7339 (tp30) REVERT: E 43 ARG cc_start: 0.7157 (mmt-90) cc_final: 0.5302 (ptm-80) REVERT: I 39 ARG cc_start: 0.7506 (ttm-80) cc_final: 0.7070 (ttp-170) REVERT: K 39 ARG cc_start: 0.7519 (ttm-80) cc_final: 0.7011 (ttm170) REVERT: K 43 ARG cc_start: 0.7245 (mmt-90) cc_final: 0.6053 (mtp-110) REVERT: M 43 ARG cc_start: 0.7138 (mmt-90) cc_final: 0.5651 (ptm-80) REVERT: O 39 ARG cc_start: 0.7742 (ttm-80) cc_final: 0.7268 (ttp-170) REVERT: O 43 ARG cc_start: 0.7338 (mmt-90) cc_final: 0.6016 (mtp-110) REVERT: S 39 ARG cc_start: 0.7503 (ttm-80) cc_final: 0.6930 (ttm170) REVERT: S 43 ARG cc_start: 0.7317 (mmt-90) cc_final: 0.5994 (ttp80) REVERT: T 12 ARG cc_start: 0.8282 (ptm-80) cc_final: 0.8078 (ptm-80) REVERT: W 28 GLN cc_start: 0.8181 (mm110) cc_final: 0.7841 (mm-40) REVERT: W 39 ARG cc_start: 0.7461 (ttm-80) cc_final: 0.6875 (ttp-170) REVERT: W 105 GLU cc_start: 0.7268 (tt0) cc_final: 0.7036 (tt0) outliers start: 16 outliers final: 13 residues processed: 147 average time/residue: 0.1576 time to fit residues: 28.9713 Evaluate side-chains 158 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain M residue 95 LYS Chi-restraints excluded: chain Q residue 20 ARG Chi-restraints excluded: chain Q residue 95 LYS Chi-restraints excluded: chain S residue 20 ARG Chi-restraints excluded: chain W residue 50 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 58 optimal weight: 0.0070 chunk 19 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 59 GLN ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN S 59 GLN S 80 ASN X 15 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.164935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.128576 restraints weight = 9833.357| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.44 r_work: 0.3222 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10824 Z= 0.096 Angle : 0.374 4.557 14520 Z= 0.196 Chirality : 0.036 0.114 1572 Planarity : 0.003 0.027 1884 Dihedral : 3.189 8.703 1452 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.39 % Allowed : 7.81 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.23), residues: 1284 helix: 2.32 (0.19), residues: 840 sheet: None (None), residues: 0 loop : -1.62 (0.19), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 39 TYR 0.004 0.001 TYR A 86 PHE 0.003 0.000 PHE T 16 TRP 0.012 0.001 TRP C 16 HIS 0.002 0.001 HIS C 89 Details of bonding type rmsd covalent geometry : bond 0.00230 (10824) covalent geometry : angle 0.37399 (14520) hydrogen bonds : bond 0.03397 ( 552) hydrogen bonds : angle 2.87726 ( 1548) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.434 Fit side-chains REVERT: A 43 ARG cc_start: 0.7103 (mmt-90) cc_final: 0.5356 (ptm-80) REVERT: C 43 ARG cc_start: 0.7149 (mmt-90) cc_final: 0.5406 (ptm-80) REVERT: E 39 ARG cc_start: 0.7697 (ttm-80) cc_final: 0.7424 (ttm110) REVERT: E 40 GLU cc_start: 0.7554 (tp30) cc_final: 0.7283 (tp30) REVERT: E 43 ARG cc_start: 0.7128 (mmt-90) cc_final: 0.5253 (ptm-80) REVERT: I 39 ARG cc_start: 0.7489 (ttm-80) cc_final: 0.7034 (ttp-170) REVERT: K 39 ARG cc_start: 0.7462 (ttm-80) cc_final: 0.6980 (ttm170) REVERT: K 43 ARG cc_start: 0.7220 (mmt-90) cc_final: 0.6037 (mtp-110) REVERT: M 43 ARG cc_start: 0.7139 (mmt-90) cc_final: 0.5644 (ptm-80) REVERT: O 28 GLN cc_start: 0.8125 (mm110) cc_final: 0.7851 (mm-40) REVERT: O 39 ARG cc_start: 0.7732 (ttm-80) cc_final: 0.7235 (ttp-170) REVERT: O 43 ARG cc_start: 0.7215 (mmt-90) cc_final: 0.5904 (mtp-110) REVERT: S 39 ARG cc_start: 0.7479 (ttm-80) cc_final: 0.6888 (ttm170) REVERT: S 43 ARG cc_start: 0.7281 (mmt-90) cc_final: 0.5960 (ttp80) REVERT: W 28 GLN cc_start: 0.8152 (mm110) cc_final: 0.7824 (mm-40) REVERT: W 39 ARG cc_start: 0.7453 (ttm-80) cc_final: 0.6847 (ttp-170) REVERT: W 105 GLU cc_start: 0.7258 (tt0) cc_final: 0.7002 (tt0) outliers start: 16 outliers final: 14 residues processed: 150 average time/residue: 0.1779 time to fit residues: 33.3551 Evaluate side-chains 161 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain M residue 95 LYS Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain Q residue 95 LYS Chi-restraints excluded: chain S residue 20 ARG Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain W residue 50 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 117 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 96 optimal weight: 0.0010 chunk 104 optimal weight: 0.2980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 59 GLN ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.160363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.122861 restraints weight = 9963.051| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.49 r_work: 0.3215 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10824 Z= 0.096 Angle : 0.376 5.818 14520 Z= 0.196 Chirality : 0.036 0.113 1572 Planarity : 0.003 0.043 1884 Dihedral : 3.152 8.595 1452 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 1.56 % Allowed : 8.16 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.23), residues: 1284 helix: 2.37 (0.19), residues: 840 sheet: None (None), residues: 0 loop : -1.61 (0.19), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 39 TYR 0.006 0.001 TYR C 29 PHE 0.003 0.000 PHE T 16 TRP 0.011 0.001 TRP G 16 HIS 0.001 0.001 HIS C 89 Details of bonding type rmsd covalent geometry : bond 0.00228 (10824) covalent geometry : angle 0.37599 (14520) hydrogen bonds : bond 0.03371 ( 552) hydrogen bonds : angle 2.85410 ( 1548) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 43 ARG cc_start: 0.7092 (mmt-90) cc_final: 0.5350 (ptm-80) REVERT: C 43 ARG cc_start: 0.7164 (mmt-90) cc_final: 0.5429 (ptm-80) REVERT: E 39 ARG cc_start: 0.7741 (ttm-80) cc_final: 0.7465 (ttm110) REVERT: E 43 ARG cc_start: 0.7166 (mmt-90) cc_final: 0.5306 (ptm-80) REVERT: K 39 ARG cc_start: 0.7499 (ttm-80) cc_final: 0.7014 (ttm170) REVERT: K 43 ARG cc_start: 0.7238 (mmt-90) cc_final: 0.6066 (mtp-110) REVERT: M 43 ARG cc_start: 0.7173 (mmt-90) cc_final: 0.5660 (ptm-80) REVERT: O 28 GLN cc_start: 0.8135 (mm110) cc_final: 0.7912 (mm-40) REVERT: O 39 ARG cc_start: 0.7771 (ttm-80) cc_final: 0.7270 (ttp-170) REVERT: O 43 ARG cc_start: 0.7250 (mmt-90) cc_final: 0.5944 (mtp-110) REVERT: S 39 ARG cc_start: 0.7504 (ttm-80) cc_final: 0.6916 (ttm170) REVERT: S 43 ARG cc_start: 0.7304 (mmt-90) cc_final: 0.5975 (ttp80) REVERT: W 28 GLN cc_start: 0.8137 (mm110) cc_final: 0.7819 (mm-40) REVERT: W 39 ARG cc_start: 0.7492 (ttm-80) cc_final: 0.6887 (ttp-170) REVERT: W 105 GLU cc_start: 0.7361 (tt0) cc_final: 0.7105 (tt0) outliers start: 18 outliers final: 13 residues processed: 150 average time/residue: 0.1685 time to fit residues: 31.5762 Evaluate side-chains 159 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain M residue 95 LYS Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain Q residue 95 LYS Chi-restraints excluded: chain S residue 20 ARG Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain W residue 50 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 16 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 59 GLN ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.164825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.128954 restraints weight = 9848.619| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.42 r_work: 0.3240 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10824 Z= 0.119 Angle : 0.409 5.060 14520 Z= 0.212 Chirality : 0.036 0.116 1572 Planarity : 0.003 0.036 1884 Dihedral : 3.335 9.723 1452 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 1.39 % Allowed : 7.99 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.23), residues: 1284 helix: 2.29 (0.19), residues: 840 sheet: None (None), residues: 0 loop : -1.70 (0.19), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 39 TYR 0.007 0.001 TYR C 29 PHE 0.005 0.001 PHE D 16 TRP 0.010 0.001 TRP G 16 HIS 0.002 0.001 HIS C 89 Details of bonding type rmsd covalent geometry : bond 0.00297 (10824) covalent geometry : angle 0.40929 (14520) hydrogen bonds : bond 0.03830 ( 552) hydrogen bonds : angle 2.94654 ( 1548) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: C 43 ARG cc_start: 0.7271 (mmt-90) cc_final: 0.5496 (ptm-80) REVERT: E 39 ARG cc_start: 0.7738 (ttm-80) cc_final: 0.7447 (ttm110) REVERT: E 43 ARG cc_start: 0.7139 (mmt-90) cc_final: 0.5360 (ptm-80) REVERT: G 69 GLN cc_start: 0.8312 (tp40) cc_final: 0.8042 (tt0) REVERT: I 105 GLU cc_start: 0.7307 (tt0) cc_final: 0.7036 (tt0) REVERT: K 39 ARG cc_start: 0.7410 (ttm-80) cc_final: 0.6937 (ttm170) REVERT: K 43 ARG cc_start: 0.7263 (mmt-90) cc_final: 0.5557 (ptm-80) REVERT: M 43 ARG cc_start: 0.7204 (mmt-90) cc_final: 0.5622 (ptm160) REVERT: O 28 GLN cc_start: 0.8151 (mm110) cc_final: 0.7938 (mm-40) REVERT: O 39 ARG cc_start: 0.7692 (ttm-80) cc_final: 0.7207 (ttp-170) REVERT: O 43 ARG cc_start: 0.7316 (mmt-90) cc_final: 0.6059 (mtp-110) REVERT: Q 17 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7248 (mt-10) REVERT: S 39 ARG cc_start: 0.7465 (ttm-80) cc_final: 0.6810 (ttm170) REVERT: W 28 GLN cc_start: 0.8110 (mm110) cc_final: 0.7755 (mm-40) REVERT: W 39 ARG cc_start: 0.7414 (ttm-80) cc_final: 0.6818 (ttp-170) REVERT: W 105 GLU cc_start: 0.7326 (tt0) cc_final: 0.7065 (tt0) outliers start: 16 outliers final: 14 residues processed: 144 average time/residue: 0.1593 time to fit residues: 28.8644 Evaluate side-chains 158 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain M residue 95 LYS Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain Q residue 95 LYS Chi-restraints excluded: chain S residue 20 ARG Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain W residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.5980 chunk 16 optimal weight: 0.0870 chunk 61 optimal weight: 0.0870 chunk 106 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 59 GLN ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.160795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.123610 restraints weight = 9969.297| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.48 r_work: 0.3227 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10824 Z= 0.086 Angle : 0.366 4.998 14520 Z= 0.190 Chirality : 0.035 0.112 1572 Planarity : 0.003 0.036 1884 Dihedral : 3.056 8.385 1452 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 1.22 % Allowed : 8.33 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.24), residues: 1284 helix: 2.44 (0.19), residues: 840 sheet: None (None), residues: 0 loop : -1.61 (0.19), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 39 TYR 0.005 0.001 TYR C 29 PHE 0.003 0.000 PHE T 16 TRP 0.013 0.001 TRP M 16 HIS 0.001 0.001 HIS Q 89 Details of bonding type rmsd covalent geometry : bond 0.00199 (10824) covalent geometry : angle 0.36625 (14520) hydrogen bonds : bond 0.03143 ( 552) hydrogen bonds : angle 2.79358 ( 1548) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 43 ARG cc_start: 0.7070 (mmt-90) cc_final: 0.5329 (ptm-80) REVERT: C 43 ARG cc_start: 0.7121 (mmt-90) cc_final: 0.5367 (ptm-80) REVERT: E 39 ARG cc_start: 0.7805 (ttm-80) cc_final: 0.7513 (ttm110) REVERT: E 43 ARG cc_start: 0.7089 (mmt-90) cc_final: 0.5264 (ptm-80) REVERT: I 105 GLU cc_start: 0.7309 (tt0) cc_final: 0.7048 (tt0) REVERT: K 39 ARG cc_start: 0.7490 (ttm-80) cc_final: 0.7005 (ttm170) REVERT: K 43 ARG cc_start: 0.7210 (mmt-90) cc_final: 0.6026 (mtp-110) REVERT: M 20 ARG cc_start: 0.8016 (ptp90) cc_final: 0.7711 (ptp90) REVERT: M 43 ARG cc_start: 0.7174 (mmt-90) cc_final: 0.5634 (ptm160) REVERT: O 28 GLN cc_start: 0.8072 (mm110) cc_final: 0.7869 (mm-40) REVERT: O 39 ARG cc_start: 0.7761 (ttm-80) cc_final: 0.7265 (ttp-170) REVERT: O 43 ARG cc_start: 0.7235 (mmt-90) cc_final: 0.6030 (mtp-110) REVERT: Q 17 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7282 (mt-10) REVERT: S 39 ARG cc_start: 0.7503 (ttm-80) cc_final: 0.6925 (ttm170) REVERT: S 43 ARG cc_start: 0.7296 (mmt-90) cc_final: 0.5966 (ttp80) REVERT: U 69 GLN cc_start: 0.8229 (tp40) cc_final: 0.8015 (tt0) REVERT: W 28 GLN cc_start: 0.8051 (mm110) cc_final: 0.7738 (mm-40) REVERT: W 39 ARG cc_start: 0.7478 (ttm-80) cc_final: 0.6818 (ttp-170) REVERT: W 105 GLU cc_start: 0.7353 (tt0) cc_final: 0.7098 (tt0) outliers start: 14 outliers final: 14 residues processed: 149 average time/residue: 0.1699 time to fit residues: 31.4728 Evaluate side-chains 162 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain M residue 95 LYS Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain Q residue 95 LYS Chi-restraints excluded: chain S residue 20 ARG Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain W residue 50 LEU Chi-restraints excluded: chain W residue 95 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 82 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 114 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 59 GLN ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.154184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.116084 restraints weight = 10175.506| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.57 r_work: 0.3167 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10824 Z= 0.169 Angle : 0.468 4.763 14520 Z= 0.240 Chirality : 0.038 0.125 1572 Planarity : 0.004 0.033 1884 Dihedral : 3.616 11.448 1452 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.30 % Allowed : 8.33 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.23), residues: 1284 helix: 2.28 (0.19), residues: 828 sheet: None (None), residues: 0 loop : -1.77 (0.19), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 39 TYR 0.008 0.001 TYR C 29 PHE 0.007 0.001 PHE D 16 TRP 0.009 0.001 TRP C 16 HIS 0.003 0.001 HIS G 33 Details of bonding type rmsd covalent geometry : bond 0.00431 (10824) covalent geometry : angle 0.46814 (14520) hydrogen bonds : bond 0.04536 ( 552) hydrogen bonds : angle 3.11880 ( 1548) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2271.49 seconds wall clock time: 39 minutes 48.08 seconds (2388.08 seconds total)