Starting phenix.real_space_refine on Fri Jan 17 06:01:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h1p_51769/01_2025/9h1p_51769.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h1p_51769/01_2025/9h1p_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9h1p_51769/01_2025/9h1p_51769.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h1p_51769/01_2025/9h1p_51769.map" model { file = "/net/cci-nas-00/data/ceres_data/9h1p_51769/01_2025/9h1p_51769.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h1p_51769/01_2025/9h1p_51769.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 4.92, per 1000 atoms: 0.46 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: 3.02 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.95 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: 2.66 Time building geometry restraints manager: 3.15 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: 0.10 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: 9.820 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.320 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.590 ------------------------------------------------------------------------------- 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= 0.232 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.023 0.004 TRP K 16 HIS 0.003 0.001 HIS W 89 PHE 0.013 0.003 PHE N 16 TYR 0.011 0.003 TYR E 29 ARG 0.025 0.003 ARG J 12 *********************** 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 : 1.155 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 43 ARG cc_start: 0.6826 (mmt-90) cc_final: 0.5690 (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: 0.5805 (ptm-80) REVERT: E 40 GLU cc_start: 0.7741 (tp30) cc_final: 0.7534 (tp30) REVERT: E 43 ARG cc_start: 0.6884 (mmt-90) cc_final: 0.5718 (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: 0.7443 (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: 0.7293 (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: 0.6063 (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: 0.7487 (tmm160) REVERT: W 43 ARG cc_start: 0.6828 (mmt-90) cc_final: 0.6124 (ttp80) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.4226 time to fit residues: 90.2039 Evaluate side-chains 150 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.162318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.127135 restraints weight = 9773.322| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.33 r_work: 0.3153 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10824 Z= 0.348 Angle : 0.580 4.716 14520 Z= 0.308 Chirality : 0.041 0.134 1572 Planarity : 0.005 0.033 1884 Dihedral : 4.770 16.420 1452 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.17 % Allowed : 3.99 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.21), residues: 1284 helix: 0.93 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -1.54 (0.18), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP U 16 HIS 0.005 0.002 HIS C 89 PHE 0.012 0.002 PHE P 16 TYR 0.013 0.002 TYR A 29 ARG 0.003 0.000 ARG C 39 *********************** 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 149 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 1.150 Fit side-chains REVERT: C 43 ARG cc_start: 0.7305 (mmt-90) cc_final: 0.5718 (ptm-80) REVERT: E 39 ARG cc_start: 0.7466 (ttm-80) cc_final: 0.7173 (ttm110) REVERT: E 40 GLU cc_start: 0.7621 (tp30) cc_final: 0.7098 (tp30) REVERT: E 43 ARG cc_start: 0.7207 (mmt-90) cc_final: 0.5527 (ptm-80) REVERT: G 90 GLN cc_start: 0.6964 (mm110) cc_final: 0.6705 (mm110) REVERT: I 39 ARG cc_start: 0.7443 (ttm-80) cc_final: 0.7155 (ttp-170) REVERT: K 39 ARG cc_start: 0.7223 (ttm-80) cc_final: 0.6817 (ttp-170) REVERT: K 40 GLU cc_start: 0.7490 (tp30) cc_final: 0.7245 (tp30) REVERT: K 43 ARG cc_start: 0.7328 (mmt-90) cc_final: 0.5743 (ptm-80) REVERT: M 43 ARG cc_start: 0.7303 (mmt-90) cc_final: 0.5742 (ptm160) REVERT: O 39 ARG cc_start: 0.7428 (ttm-80) cc_final: 0.7008 (ttp-170) REVERT: O 43 ARG cc_start: 0.7470 (mmt-90) cc_final: 0.6088 (mtp-110) REVERT: Q 90 GLN cc_start: 0.7034 (mm110) cc_final: 0.6827 (mm110) REVERT: S 39 ARG cc_start: 0.7247 (ttm-80) cc_final: 0.6734 (ttm170) REVERT: W 39 ARG cc_start: 0.7488 (ttm-80) cc_final: 0.6887 (tmm160) REVERT: W 105 GLU cc_start: 0.7213 (tt0) cc_final: 0.6949 (tt0) outliers start: 2 outliers final: 1 residues processed: 147 average time/residue: 0.3915 time to fit residues: 71.8342 Evaluate side-chains 138 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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 2 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 115 optimal weight: 0.6980 chunk 111 optimal weight: 0.0010 chunk 5 optimal weight: 0.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 O 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 = 0.3814 r_free = 0.3814 target = 0.161649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123702 restraints weight = 10046.962| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.57 r_work: 0.3205 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.1886 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= 0.150 Angle : 0.406 4.644 14520 Z= 0.217 Chirality : 0.036 0.118 1572 Planarity : 0.004 0.033 1884 Dihedral : 3.744 11.531 1452 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.78 % Allowed : 4.86 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.22), residues: 1284 helix: 1.57 (0.19), residues: 852 sheet: None (None), residues: 0 loop : -1.58 (0.19), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 16 HIS 0.001 0.001 HIS Q 89 PHE 0.004 0.001 PHE B 16 TYR 0.008 0.001 TYR A 29 ARG 0.005 0.000 ARG Q 39 *********************** 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 165 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 1.138 Fit side-chains REVERT: A 40 GLU cc_start: 0.7746 (tp30) cc_final: 0.7467 (tp30) REVERT: A 43 ARG cc_start: 0.7062 (mmt-90) cc_final: 0.5356 (ptm-80) REVERT: C 43 ARG cc_start: 0.7085 (mmt-90) cc_final: 0.5524 (ptm-80) REVERT: E 39 ARG cc_start: 0.7539 (ttm-80) cc_final: 0.7228 (ttm110) REVERT: E 40 GLU cc_start: 0.7479 (tp30) cc_final: 0.7035 (tp30) REVERT: E 43 ARG cc_start: 0.7126 (mmt-90) cc_final: 0.5292 (ptm-80) REVERT: G 90 GLN cc_start: 0.6755 (mm110) cc_final: 0.6470 (mm110) REVERT: I 39 ARG cc_start: 0.7477 (ttm-80) cc_final: 0.7124 (ttp-170) REVERT: I 43 ARG cc_start: 0.7125 (mmt-90) cc_final: 0.5453 (ptm160) REVERT: K 28 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7791 (mm-40) REVERT: K 39 ARG cc_start: 0.7283 (ttm-80) cc_final: 0.6861 (ttp-170) REVERT: K 43 ARG cc_start: 0.7143 (mmt-90) cc_final: 0.5958 (mtp-110) REVERT: M 43 ARG cc_start: 0.7110 (mmt-90) cc_final: 0.5736 (ttp80) REVERT: O 39 ARG cc_start: 0.7566 (ttm-80) cc_final: 0.7080 (ttp-170) REVERT: O 43 ARG cc_start: 0.7323 (mmt-90) cc_final: 0.6075 (mtp-110) REVERT: Q 43 ARG cc_start: 0.7060 (mmt-90) cc_final: 0.5238 (ptm-80) REVERT: Q 90 GLN cc_start: 0.6916 (mm110) cc_final: 0.6677 (mm110) REVERT: S 39 ARG cc_start: 0.7358 (ttm-80) cc_final: 0.6881 (ttm170) REVERT: S 43 ARG cc_start: 0.7267 (mmt-90) cc_final: 0.5857 (ttp80) REVERT: U 43 ARG cc_start: 0.7083 (mmt-90) cc_final: 0.5475 (ttp80) REVERT: W 28 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7621 (mm-40) REVERT: W 39 ARG cc_start: 0.7434 (ttm-80) cc_final: 0.6924 (ttp-170) REVERT: W 43 ARG cc_start: 0.6935 (mmt-90) cc_final: 0.5587 (ttp80) REVERT: W 105 GLU cc_start: 0.7275 (tt0) cc_final: 0.7026 (tt0) outliers start: 9 outliers final: 6 residues processed: 157 average time/residue: 0.4081 time to fit residues: 79.5329 Evaluate side-chains 153 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain Q residue 20 ARG Chi-restraints excluded: chain S residue 20 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 0.2980 chunk 95 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 S 80 ASN ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.159423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.121233 restraints weight = 10093.386| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.58 r_work: 0.3175 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10824 Z= 0.175 Angle : 0.411 4.552 14520 Z= 0.216 Chirality : 0.037 0.116 1572 Planarity : 0.004 0.027 1884 Dihedral : 3.555 11.029 1452 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 1.72 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.23), residues: 1284 helix: 1.93 (0.19), residues: 852 sheet: None (None), residues: 0 loop : -1.67 (0.19), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 16 HIS 0.002 0.001 HIS C 89 PHE 0.005 0.001 PHE D 16 TYR 0.007 0.001 TYR A 29 ARG 0.005 0.000 ARG U 39 *********************** 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 155 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 1.177 Fit side-chains REVERT: A 40 GLU cc_start: 0.7685 (tp30) cc_final: 0.7458 (tp30) REVERT: C 43 ARG cc_start: 0.7280 (mmt-90) cc_final: 0.5688 (ptm-80) REVERT: E 39 ARG cc_start: 0.7695 (ttm-80) cc_final: 0.7378 (ttm110) REVERT: E 40 GLU cc_start: 0.7589 (tp30) cc_final: 0.7180 (tp30) REVERT: E 43 ARG cc_start: 0.7178 (mmt-90) cc_final: 0.5292 (ptm-80) REVERT: E 105 GLU cc_start: 0.7177 (tt0) cc_final: 0.6972 (tt0) REVERT: G 90 GLN cc_start: 0.6923 (mm110) cc_final: 0.6640 (mm110) REVERT: I 39 ARG cc_start: 0.7527 (ttm-80) cc_final: 0.7149 (ttp-170) REVERT: I 43 ARG cc_start: 0.7130 (mmt-90) cc_final: 0.5367 (ptm160) REVERT: K 28 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7771 (mm-40) REVERT: K 39 ARG cc_start: 0.7469 (ttm-80) cc_final: 0.6972 (ttm170) REVERT: K 43 ARG cc_start: 0.7213 (mmt-90) cc_final: 0.5854 (mtp-110) REVERT: M 43 ARG cc_start: 0.7165 (mmt-90) cc_final: 0.5654 (ptm160) REVERT: O 39 ARG cc_start: 0.7711 (ttm-80) cc_final: 0.7250 (ttp-170) REVERT: O 43 ARG cc_start: 0.7358 (mmt-90) cc_final: 0.6080 (mtp-110) REVERT: Q 90 GLN cc_start: 0.6986 (mm110) cc_final: 0.6736 (mm110) REVERT: S 39 ARG cc_start: 0.7425 (ttm-80) cc_final: 0.6897 (ttm170) REVERT: S 43 ARG cc_start: 0.7321 (mmt-90) cc_final: 0.5974 (ttp80) REVERT: T 12 ARG cc_start: 0.8275 (ptm-80) cc_final: 0.8034 (ptm-80) REVERT: W 28 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7644 (mm-40) REVERT: W 39 ARG cc_start: 0.7445 (ttm-80) cc_final: 0.6876 (ttp-170) REVERT: W 105 GLU cc_start: 0.7262 (tt0) cc_final: 0.6994 (tt0) outliers start: 10 outliers final: 8 residues processed: 145 average time/residue: 0.3918 time to fit residues: 71.0918 Evaluate side-chains 149 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 I residue 38 SER Chi-restraints excluded: chain Q residue 20 ARG Chi-restraints excluded: chain Q residue 95 LYS Chi-restraints excluded: chain S residue 20 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 105 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 S 59 GLN S 80 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.158271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.121035 restraints weight = 9993.267| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.49 r_work: 0.3194 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2338 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= 0.183 Angle : 0.405 4.526 14520 Z= 0.212 Chirality : 0.037 0.115 1572 Planarity : 0.003 0.025 1884 Dihedral : 3.460 10.200 1452 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.04 % Allowed : 6.60 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.23), residues: 1284 helix: 2.12 (0.19), residues: 840 sheet: None (None), residues: 0 loop : -1.83 (0.18), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 16 HIS 0.002 0.001 HIS C 89 PHE 0.005 0.001 PHE D 16 TYR 0.006 0.001 TYR A 29 ARG 0.007 0.000 ARG G 39 *********************** 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 155 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 1.145 Fit side-chains REVERT: A 40 GLU cc_start: 0.7665 (tp30) cc_final: 0.7441 (tp30) REVERT: C 43 ARG cc_start: 0.7242 (mmt-90) cc_final: 0.5658 (ptm-80) REVERT: E 39 ARG cc_start: 0.7797 (ttm-80) cc_final: 0.7472 (ttm110) REVERT: E 40 GLU cc_start: 0.7632 (tp30) cc_final: 0.7279 (tp30) REVERT: E 43 ARG cc_start: 0.7130 (mmt-90) cc_final: 0.5294 (ptm-80) REVERT: G 90 GLN cc_start: 0.7033 (mm110) cc_final: 0.6717 (mm110) REVERT: I 39 ARG cc_start: 0.7553 (ttm-80) cc_final: 0.7120 (ttp-170) REVERT: K 28 GLN cc_start: 0.8274 (mm-40) cc_final: 0.7805 (mm-40) REVERT: K 39 ARG cc_start: 0.7506 (ttm-80) cc_final: 0.7014 (ttm170) REVERT: K 43 ARG cc_start: 0.7222 (mmt-90) cc_final: 0.5655 (ptm-80) REVERT: M 43 ARG cc_start: 0.7201 (mmt-90) cc_final: 0.5656 (ptm-80) REVERT: O 39 ARG cc_start: 0.7769 (ttm-80) cc_final: 0.7306 (ttp-170) REVERT: O 43 ARG cc_start: 0.7391 (mmt-90) cc_final: 0.6042 (mtp-110) REVERT: S 39 ARG cc_start: 0.7501 (ttm-80) cc_final: 0.6928 (ttm170) REVERT: S 43 ARG cc_start: 0.7352 (mmt-90) cc_final: 0.6082 (ttp80) REVERT: T 12 ARG cc_start: 0.8291 (ptm-80) cc_final: 0.8081 (ptm-80) REVERT: W 28 GLN cc_start: 0.8101 (mm-40) cc_final: 0.7701 (mm-40) REVERT: W 39 ARG cc_start: 0.7472 (ttm-80) cc_final: 0.6915 (tmm160) REVERT: W 105 GLU cc_start: 0.7277 (tt0) cc_final: 0.7048 (tt0) outliers start: 12 outliers final: 10 residues processed: 144 average time/residue: 0.4046 time to fit residues: 72.6312 Evaluate side-chains 152 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 41 optimal weight: 0.9990 chunk 6 optimal weight: 0.0040 chunk 69 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 108 optimal weight: 0.0020 chunk 115 optimal weight: 1.9990 chunk 44 optimal weight: 0.1980 chunk 71 optimal weight: 0.5980 overall best weight: 0.3602 ------------------------------------------------------------------------------- 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 S 28 GLN S 59 GLN ** 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 = 0.3812 r_free = 0.3812 target = 0.161698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.124733 restraints weight = 10035.136| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.49 r_work: 0.3246 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10824 Z= 0.111 Angle : 0.353 4.522 14520 Z= 0.185 Chirality : 0.035 0.115 1572 Planarity : 0.003 0.028 1884 Dihedral : 3.052 8.806 1452 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.22 % Allowed : 7.73 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.23), residues: 1284 helix: 2.25 (0.19), residues: 852 sheet: None (None), residues: 0 loop : -1.58 (0.19), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 16 HIS 0.001 0.000 HIS M 89 PHE 0.002 0.000 PHE T 16 TYR 0.004 0.001 TYR M 86 ARG 0.007 0.000 ARG G 39 *********************** 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 174 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 1.248 Fit side-chains REVERT: A 40 GLU cc_start: 0.7628 (tp30) cc_final: 0.7390 (tp30) REVERT: A 43 ARG cc_start: 0.7015 (mmt-90) cc_final: 0.5336 (ptm-80) REVERT: C 43 ARG cc_start: 0.7041 (mmt-90) cc_final: 0.5361 (ptm-80) REVERT: E 39 ARG cc_start: 0.7795 (ttm-80) cc_final: 0.7442 (ttm110) REVERT: E 43 ARG cc_start: 0.7068 (mmt-90) cc_final: 0.5315 (ptm-80) REVERT: I 39 ARG cc_start: 0.7519 (ttm-80) cc_final: 0.7103 (ttp-170) REVERT: I 43 ARG cc_start: 0.7063 (mmt-90) cc_final: 0.5397 (ptm160) REVERT: K 28 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7744 (mm-40) REVERT: K 39 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.7030 (ttm170) REVERT: K 43 ARG cc_start: 0.7178 (mmt-90) cc_final: 0.6023 (mtp-110) REVERT: M 43 ARG cc_start: 0.7115 (mmt-90) cc_final: 0.5848 (ttp80) REVERT: O 39 ARG cc_start: 0.7769 (ttm-80) cc_final: 0.7286 (ttp-170) REVERT: O 43 ARG cc_start: 0.7246 (mmt-90) cc_final: 0.6026 (mtp-110) REVERT: S 39 ARG cc_start: 0.7508 (ttm-80) cc_final: 0.6935 (ttm170) REVERT: S 43 ARG cc_start: 0.7276 (mmt-90) cc_final: 0.5844 (ttp80) REVERT: T 12 ARG cc_start: 0.8229 (ptm-80) cc_final: 0.8016 (ptm-80) REVERT: U 43 ARG cc_start: 0.6977 (mmt-90) cc_final: 0.5400 (ttp80) REVERT: W 28 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7664 (mm-40) REVERT: W 39 ARG cc_start: 0.7462 (ttm-80) cc_final: 0.6971 (tmm160) REVERT: W 43 ARG cc_start: 0.6940 (mmt-90) cc_final: 0.5349 (ptm-80) REVERT: W 105 GLU cc_start: 0.7280 (tt0) cc_final: 0.7025 (tt0) outliers start: 14 outliers final: 9 residues processed: 161 average time/residue: 0.4036 time to fit residues: 80.3833 Evaluate side-chains 163 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain C residue 95 LYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 104 optimal weight: 0.2980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 59 GLN O 28 GLN S 28 GLN S 59 GLN S 80 ASN ** 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 = 0.3828 r_free = 0.3828 target = 0.159478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.123481 restraints weight = 10099.200| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.45 r_work: 0.3183 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2533 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= 0.218 Angle : 0.425 4.640 14520 Z= 0.220 Chirality : 0.037 0.119 1572 Planarity : 0.003 0.029 1884 Dihedral : 3.433 10.083 1452 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 1.22 % Allowed : 8.25 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.23), residues: 1284 helix: 2.23 (0.19), residues: 840 sheet: None (None), residues: 0 loop : -1.83 (0.18), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 16 HIS 0.002 0.001 HIS C 89 PHE 0.005 0.001 PHE F 16 TYR 0.007 0.001 TYR C 29 ARG 0.007 0.000 ARG G 39 *********************** 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 157 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 1.225 Fit side-chains REVERT: A 40 GLU cc_start: 0.7684 (tp30) cc_final: 0.7472 (tp30) REVERT: C 43 ARG cc_start: 0.7309 (mmt-90) cc_final: 0.5557 (ptm-80) REVERT: E 39 ARG cc_start: 0.7805 (ttm-80) cc_final: 0.7440 (ttm110) REVERT: I 39 ARG cc_start: 0.7537 (ttm-80) cc_final: 0.7086 (ttp-170) REVERT: K 28 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7768 (mm-40) REVERT: K 39 ARG cc_start: 0.7458 (ttm-80) cc_final: 0.6968 (ttm170) REVERT: K 43 ARG cc_start: 0.7331 (mmt-90) cc_final: 0.5607 (ptm-80) REVERT: M 43 ARG cc_start: 0.7215 (mmt-90) cc_final: 0.5468 (ptm160) REVERT: O 28 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7464 (mm110) REVERT: O 39 ARG cc_start: 0.7731 (ttm-80) cc_final: 0.7258 (ttp-170) REVERT: O 43 ARG cc_start: 0.7408 (mmt-90) cc_final: 0.6040 (mtp-110) REVERT: S 39 ARG cc_start: 0.7501 (ttm-80) cc_final: 0.6838 (ttm170) REVERT: W 28 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7678 (mm-40) REVERT: W 39 ARG cc_start: 0.7426 (ttm-80) cc_final: 0.6832 (ttp-170) REVERT: W 105 GLU cc_start: 0.7304 (tt0) cc_final: 0.7053 (tt0) outliers start: 14 outliers final: 12 residues processed: 144 average time/residue: 0.3843 time to fit residues: 69.4858 Evaluate side-chains 155 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E residue 38 SER 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 O residue 28 GLN Chi-restraints excluded: chain O residue 46 VAL 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 109 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 59 GLN O 28 GLN S 28 GLN S 59 GLN S 80 ASN ** 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 = 0.3769 r_free = 0.3769 target = 0.157580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.119611 restraints weight = 10048.318| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.54 r_work: 0.3125 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 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 : 0.003 0.024 10824 Z= 0.183 Angle : 0.400 4.534 14520 Z= 0.208 Chirality : 0.036 0.114 1572 Planarity : 0.003 0.027 1884 Dihedral : 3.327 9.152 1452 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.48 % Allowed : 8.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.23), residues: 1284 helix: 2.25 (0.19), residues: 840 sheet: None (None), residues: 0 loop : -1.81 (0.19), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 16 HIS 0.002 0.001 HIS C 89 PHE 0.005 0.001 PHE D 16 TYR 0.006 0.001 TYR C 29 ARG 0.006 0.000 ARG G 39 *********************** 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 163 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 1.141 Fit side-chains revert: symmetry clash REVERT: A 40 GLU cc_start: 0.7587 (tp30) cc_final: 0.7362 (tp30) REVERT: C 43 ARG cc_start: 0.7275 (mmt-90) cc_final: 0.5492 (ptm-80) REVERT: E 39 ARG cc_start: 0.7786 (ttm-80) cc_final: 0.7445 (ttm110) REVERT: E 43 ARG cc_start: 0.7120 (mmt-90) cc_final: 0.5335 (ptm-80) REVERT: I 105 GLU cc_start: 0.7298 (tt0) cc_final: 0.7027 (tt0) REVERT: K 28 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7681 (mm-40) REVERT: K 39 ARG cc_start: 0.7433 (ttm-80) cc_final: 0.6946 (ttm170) REVERT: K 43 ARG cc_start: 0.7283 (mmt-90) cc_final: 0.5544 (ptm-80) REVERT: M 43 ARG cc_start: 0.7279 (mmt-90) cc_final: 0.5632 (ptm160) REVERT: O 28 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7407 (mm110) REVERT: O 39 ARG cc_start: 0.7711 (ttm-80) cc_final: 0.7217 (ttp-170) REVERT: O 43 ARG cc_start: 0.7321 (mmt-90) cc_final: 0.6054 (mtp-110) REVERT: S 39 ARG cc_start: 0.7485 (ttm-80) cc_final: 0.6801 (ttm170) REVERT: W 28 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7644 (mm-40) REVERT: W 39 ARG cc_start: 0.7425 (ttm-80) cc_final: 0.6808 (ttp-170) REVERT: W 105 GLU cc_start: 0.7318 (tt0) cc_final: 0.7070 (tt0) outliers start: 17 outliers final: 13 residues processed: 150 average time/residue: 0.3771 time to fit residues: 71.0394 Evaluate side-chains 160 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 68 LEU Chi-restraints excluded: chain M residue 95 LYS Chi-restraints excluded: chain O residue 28 GLN 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 2 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 chunk 55 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 111 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.162756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.124014 restraints weight = 10038.346| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.61 r_work: 0.3232 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10824 Z= 0.143 Angle : 0.383 5.884 14520 Z= 0.198 Chirality : 0.036 0.113 1572 Planarity : 0.003 0.042 1884 Dihedral : 3.177 8.661 1452 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.22 % Allowed : 8.85 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.23), residues: 1284 helix: 2.35 (0.19), residues: 840 sheet: None (None), residues: 0 loop : -1.74 (0.19), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 16 HIS 0.001 0.001 HIS C 89 PHE 0.003 0.000 PHE D 16 TYR 0.005 0.001 TYR C 29 ARG 0.010 0.000 ARG G 39 *********************** 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 162 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: A 40 GLU cc_start: 0.7505 (tp30) cc_final: 0.7292 (tp30) REVERT: C 43 ARG cc_start: 0.7156 (mmt-90) cc_final: 0.5404 (ptm-80) REVERT: E 39 ARG cc_start: 0.7724 (ttm-80) cc_final: 0.7395 (ttm110) REVERT: E 43 ARG cc_start: 0.7082 (mmt-90) cc_final: 0.5176 (ptm-80) REVERT: G 69 GLN cc_start: 0.8312 (tt0) cc_final: 0.8102 (tp40) REVERT: I 105 GLU cc_start: 0.7282 (tt0) cc_final: 0.7019 (tt0) REVERT: K 28 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7644 (mm-40) REVERT: K 39 ARG cc_start: 0.7426 (ttm-80) cc_final: 0.6930 (ttm170) REVERT: K 43 ARG cc_start: 0.7181 (mmt-90) cc_final: 0.5946 (mtp-110) REVERT: M 43 ARG cc_start: 0.7206 (mmt-90) cc_final: 0.5592 (ptm-80) REVERT: O 39 ARG cc_start: 0.7660 (ttm-80) cc_final: 0.7168 (ttp-170) REVERT: O 43 ARG cc_start: 0.7262 (mmt-90) cc_final: 0.5840 (mtp-110) REVERT: S 39 ARG cc_start: 0.7438 (ttm-80) cc_final: 0.6824 (ttm170) REVERT: S 43 ARG cc_start: 0.7283 (mmt-90) cc_final: 0.5972 (ttp80) REVERT: U 69 GLN cc_start: 0.8227 (tp40) cc_final: 0.7971 (tt0) REVERT: W 28 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7571 (mm-40) REVERT: W 39 ARG cc_start: 0.7331 (ttm-80) cc_final: 0.6696 (ttp-170) REVERT: W 105 GLU cc_start: 0.7240 (tt0) cc_final: 0.6999 (tt0) outliers start: 14 outliers final: 13 residues processed: 149 average time/residue: 0.3868 time to fit residues: 71.9679 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 : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 O residue 46 VAL 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 46 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 106 optimal weight: 0.3980 chunk 110 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 84 optimal weight: 0.0470 chunk 104 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.159022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.121555 restraints weight = 10067.776| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.50 r_work: 0.3175 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10824 Z= 0.140 Angle : 0.380 5.558 14520 Z= 0.196 Chirality : 0.036 0.111 1572 Planarity : 0.003 0.040 1884 Dihedral : 3.079 9.692 1452 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 1.30 % Allowed : 8.77 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.24), residues: 1284 helix: 2.30 (0.19), residues: 852 sheet: None (None), residues: 0 loop : -1.91 (0.19), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 16 HIS 0.001 0.001 HIS O 33 PHE 0.003 0.000 PHE D 16 TYR 0.004 0.001 TYR C 29 ARG 0.010 0.000 ARG G 39 ********************** 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 168 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: A 43 ARG cc_start: 0.7113 (mmt-90) cc_final: 0.5322 (ptm-80) REVERT: C 43 ARG cc_start: 0.7179 (mmt-90) cc_final: 0.5392 (ptm-80) REVERT: E 39 ARG cc_start: 0.7771 (ttm-80) cc_final: 0.7410 (ttm110) REVERT: E 43 ARG cc_start: 0.7070 (mmt-90) cc_final: 0.5212 (ptm-80) REVERT: I 105 GLU cc_start: 0.7327 (tt0) cc_final: 0.7067 (tt0) REVERT: K 28 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7698 (mm-40) REVERT: K 39 ARG cc_start: 0.7478 (ttm-80) cc_final: 0.6990 (ttm170) REVERT: K 43 ARG cc_start: 0.7229 (mmt-90) cc_final: 0.6020 (mtp-110) REVERT: M 20 ARG cc_start: 0.7951 (ptp90) cc_final: 0.7662 (ptp90) REVERT: M 43 ARG cc_start: 0.7250 (mmt-90) cc_final: 0.5655 (ptm160) REVERT: O 28 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7813 (mm-40) REVERT: O 39 ARG cc_start: 0.7753 (ttm-80) cc_final: 0.7255 (ttp-170) REVERT: O 43 ARG cc_start: 0.7246 (mmt-90) cc_final: 0.6024 (mtp-110) REVERT: Q 17 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7275 (mt-10) REVERT: S 39 ARG cc_start: 0.7523 (ttm-80) cc_final: 0.6908 (ttm170) REVERT: S 43 ARG cc_start: 0.7275 (mmt-90) cc_final: 0.6013 (ttp80) REVERT: T 12 ARG cc_start: 0.8110 (ptm-80) cc_final: 0.7891 (ttp80) REVERT: W 28 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7648 (mm-40) REVERT: W 39 ARG cc_start: 0.7416 (ttm-80) cc_final: 0.6818 (ttp-170) REVERT: W 105 GLU cc_start: 0.7355 (tt0) cc_final: 0.7107 (tt0) outliers start: 15 outliers final: 13 residues processed: 156 average time/residue: 0.3868 time to fit residues: 75.2116 Evaluate side-chains 165 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 46 VAL 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 104 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 31 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 108 optimal weight: 0.0570 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.6700 ------------------------------------------------------------------------------- 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 S 80 ASN ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.158829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.120750 restraints weight = 10086.629| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.57 r_work: 0.3135 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10824 Z= 0.165 Angle : 0.399 6.148 14520 Z= 0.205 Chirality : 0.036 0.114 1572 Planarity : 0.003 0.039 1884 Dihedral : 3.191 9.952 1452 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 1.30 % Allowed : 8.51 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.24), residues: 1284 helix: 2.26 (0.19), residues: 852 sheet: None (None), residues: 0 loop : -1.95 (0.18), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 16 HIS 0.002 0.001 HIS G 33 PHE 0.004 0.001 PHE D 16 TYR 0.005 0.001 TYR C 29 ARG 0.009 0.000 ARG G 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4982.97 seconds wall clock time: 90 minutes 54.05 seconds (5454.05 seconds total)