Starting phenix.real_space_refine on Sun Dec 29 11:29:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h1p_51769/12_2024/9h1p_51769.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h1p_51769/12_2024/9h1p_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_51769/12_2024/9h1p_51769.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h1p_51769/12_2024/9h1p_51769.map" model { file = "/net/cci-nas-00/data/ceres_data/9h1p_51769/12_2024/9h1p_51769.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h1p_51769/12_2024/9h1p_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.15, per 1000 atoms: 0.48 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: 2.76 Conformation dependent library (CDL) restraints added in 1.3 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: 1.00 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: 2.74 Time building geometry restraints manager: 3.17 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: 0.00 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: 10.980 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 24.350 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.630 ------------------------------------------------------------------------------- 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 : 1.294 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: 0.4490 time to fit residues: 96.1705 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 : 1.156 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 : 1.341 Fit side-chains REVERT: C 43 ARG cc_start: 0.7235 (mmt-90) cc_final: 0.6002 (ptm-80) REVERT: E 39 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7548 (ttm110) REVERT: E 40 GLU cc_start: 0.7839 (tp30) cc_final: 0.7404 (tp30) REVERT: E 43 ARG cc_start: 0.7110 (mmt-90) cc_final: 0.5892 (ptm-80) REVERT: G 90 GLN cc_start: 0.7462 (mm110) cc_final: 0.7131 (mm110) REVERT: K 39 ARG cc_start: 0.7793 (ttm-80) cc_final: 0.7438 (ttp-170) REVERT: K 43 ARG cc_start: 0.7160 (mmt-90) cc_final: 0.6042 (ptm-80) REVERT: M 43 ARG cc_start: 0.7203 (mmt-90) cc_final: 0.6069 (ptm160) REVERT: O 39 ARG cc_start: 0.7916 (ttm-80) cc_final: 0.7562 (ttp-170) REVERT: O 43 ARG cc_start: 0.7320 (mmt-90) cc_final: 0.6445 (mtp-110) REVERT: Q 90 GLN cc_start: 0.7505 (mm110) cc_final: 0.7287 (mm110) REVERT: S 39 ARG cc_start: 0.7835 (ttm-80) cc_final: 0.7501 (ttm170) REVERT: W 39 ARG cc_start: 0.7954 (ttm-80) cc_final: 0.7637 (tmm160) REVERT: W 105 GLU cc_start: 0.7237 (tt0) cc_final: 0.6988 (tt0) outliers start: 2 outliers final: 1 residues processed: 147 average time/residue: 0.3892 time to fit residues: 72.2821 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 : 1.382 ------------------------------------------------------------------------------- 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 60 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 108 optimal weight: 0.0870 chunk 37 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 S 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1918 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= 0.177 Angle : 0.424 4.600 14520 Z= 0.226 Chirality : 0.037 0.118 1572 Planarity : 0.004 0.034 1884 Dihedral : 3.859 11.828 1452 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.87 % Allowed : 4.95 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.75 (0.23), residues: 1284 helix: 1.53 (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 0.015 0.002 TRP I 16 HIS 0.002 0.001 HIS C 89 PHE 0.005 0.001 PHE F 16 TYR 0.009 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 161 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 1.256 Fit side-chains REVERT: A 40 GLU cc_start: 0.7894 (tp30) cc_final: 0.7677 (tp30) REVERT: A 43 ARG cc_start: 0.7025 (mmt-90) cc_final: 0.5832 (ptm-80) REVERT: C 43 ARG cc_start: 0.7097 (mmt-90) cc_final: 0.5950 (ptm-80) REVERT: E 39 ARG cc_start: 0.7954 (ttm-80) cc_final: 0.7630 (ttm110) REVERT: E 40 GLU cc_start: 0.7753 (tp30) cc_final: 0.7376 (tp30) REVERT: E 43 ARG cc_start: 0.7091 (mmt-90) cc_final: 0.5731 (ptm-80) REVERT: E 105 GLU cc_start: 0.7127 (tt0) cc_final: 0.6917 (tt0) REVERT: G 90 GLN cc_start: 0.7361 (mm110) cc_final: 0.7025 (mm110) REVERT: I 39 ARG cc_start: 0.8320 (ttp-170) cc_final: 0.7980 (ttp-170) REVERT: I 43 ARG cc_start: 0.7086 (mmt-90) cc_final: 0.5743 (ptm160) REVERT: K 28 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8054 (mm-40) REVERT: K 39 ARG cc_start: 0.7958 (ttm-80) cc_final: 0.7603 (ttp-170) REVERT: K 43 ARG cc_start: 0.7069 (mmt-90) cc_final: 0.6362 (mtp-110) REVERT: M 43 ARG cc_start: 0.7090 (mmt-90) cc_final: 0.6057 (ptm160) REVERT: O 39 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7667 (ttp-170) REVERT: O 43 ARG cc_start: 0.7200 (mmt-90) cc_final: 0.6450 (mtp-110) REVERT: Q 90 GLN cc_start: 0.7418 (mm110) cc_final: 0.7183 (mm110) REVERT: S 39 ARG cc_start: 0.7926 (ttm-80) cc_final: 0.7523 (ttm170) REVERT: S 43 ARG cc_start: 0.7139 (mmt-90) cc_final: 0.6264 (ttp80) REVERT: U 43 ARG cc_start: 0.7196 (mmt-90) cc_final: 0.6025 (ttp80) REVERT: W 39 ARG cc_start: 0.7956 (ttm-80) cc_final: 0.7657 (ttp-170) REVERT: W 105 GLU cc_start: 0.7290 (tt0) cc_final: 0.7045 (tt0) outliers start: 10 outliers final: 6 residues processed: 152 average time/residue: 0.4141 time to fit residues: 78.0792 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 : 1.438 ------------------------------------------------------------------------------- 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 107 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 59 GLN O 59 GLN S 28 GLN S 59 GLN S 80 ASN X 15 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2214 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= 0.201 Angle : 0.427 4.563 14520 Z= 0.225 Chirality : 0.037 0.117 1572 Planarity : 0.004 0.029 1884 Dihedral : 3.672 11.350 1452 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.04 % Allowed : 6.34 % 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 (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: 1.03 (0.23), residues: 1284 helix: 1.83 (0.19), residues: 852 sheet: None (None), residues: 0 loop : -1.76 (0.19), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 16 HIS 0.002 0.001 HIS C 89 PHE 0.006 0.001 PHE D 16 TYR 0.007 0.001 TYR A 29 ARG 0.005 0.000 ARG Q 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 153 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 1.337 Fit side-chains REVERT: C 43 ARG cc_start: 0.7161 (mmt-90) cc_final: 0.5968 (ptm-80) REVERT: E 39 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7768 (ttm110) REVERT: E 40 GLU cc_start: 0.7779 (tp30) cc_final: 0.7467 (tp30) REVERT: E 43 ARG cc_start: 0.7066 (mmt-90) cc_final: 0.5617 (ptm-80) REVERT: G 90 GLN cc_start: 0.7459 (mm110) cc_final: 0.7142 (mm110) REVERT: K 28 GLN cc_start: 0.8420 (mm-40) cc_final: 0.8083 (mm-40) REVERT: K 39 ARG cc_start: 0.8008 (ttm-80) cc_final: 0.7619 (ttm170) REVERT: K 43 ARG cc_start: 0.7128 (mmt-90) cc_final: 0.6032 (ptm-80) REVERT: M 43 ARG cc_start: 0.7133 (mmt-90) cc_final: 0.6030 (ptm-80) REVERT: O 39 ARG cc_start: 0.8138 (ttm-80) cc_final: 0.7811 (ttp-170) REVERT: O 43 ARG cc_start: 0.7231 (mmt-90) cc_final: 0.6433 (mtp-110) REVERT: Q 90 GLN cc_start: 0.7556 (mm110) cc_final: 0.7313 (mm110) REVERT: S 39 ARG cc_start: 0.7991 (ttm-80) cc_final: 0.7550 (ttm170) REVERT: S 43 ARG cc_start: 0.7181 (mmt-90) cc_final: 0.6329 (ttp80) REVERT: W 39 ARG cc_start: 0.7957 (ttm-80) cc_final: 0.7663 (ttp-170) REVERT: W 105 GLU cc_start: 0.7269 (tt0) cc_final: 0.6995 (tt0) outliers start: 12 outliers final: 9 residues processed: 142 average time/residue: 0.4074 time to fit residues: 72.6543 Evaluate side-chains 146 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 1.305 ------------------------------------------------------------------------------- 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 G residue 95 LYS 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 96 optimal weight: 0.0870 chunk 65 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 47 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 59 GLN O 59 GLN S 28 GLN S 59 GLN S 80 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2346 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= 0.156 Angle : 0.384 4.513 14520 Z= 0.202 Chirality : 0.036 0.115 1572 Planarity : 0.003 0.025 1884 Dihedral : 3.382 10.241 1452 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.13 % Allowed : 6.42 % Favored : 92.45 % 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: 1.28 (0.23), residues: 1284 helix: 2.04 (0.19), residues: 852 sheet: None (None), residues: 0 loop : -1.70 (0.19), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 16 HIS 0.001 0.001 HIS C 89 PHE 0.003 0.001 PHE D 16 TYR 0.005 0.001 TYR A 29 ARG 0.008 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 159 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 1.214 Fit side-chains REVERT: A 43 ARG cc_start: 0.7052 (mmt-90) cc_final: 0.5734 (ptm-80) REVERT: C 43 ARG cc_start: 0.7102 (mmt-90) cc_final: 0.5903 (ptm-80) REVERT: E 39 ARG cc_start: 0.8138 (ttm-80) cc_final: 0.7791 (ttm110) REVERT: E 40 GLU cc_start: 0.7797 (tp30) cc_final: 0.7524 (tp30) REVERT: E 43 ARG cc_start: 0.7043 (mmt-90) cc_final: 0.5694 (ptm-80) REVERT: G 90 GLN cc_start: 0.7426 (mm110) cc_final: 0.7076 (mm110) REVERT: K 28 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8061 (mm-40) REVERT: K 39 ARG cc_start: 0.8020 (ttm-80) cc_final: 0.7633 (ttm170) REVERT: K 43 ARG cc_start: 0.7057 (mmt-90) cc_final: 0.6394 (mtp-110) REVERT: M 43 ARG cc_start: 0.7104 (mmt-90) cc_final: 0.6025 (ptm160) REVERT: O 39 ARG cc_start: 0.8150 (ttm-80) cc_final: 0.7819 (ttp-170) REVERT: O 43 ARG cc_start: 0.7141 (mmt-90) cc_final: 0.6422 (mtp-110) REVERT: S 39 ARG cc_start: 0.8017 (ttm-80) cc_final: 0.7539 (ttm170) REVERT: S 43 ARG cc_start: 0.7132 (mmt-90) cc_final: 0.6242 (ttp80) REVERT: T 12 ARG cc_start: 0.8667 (ptm-80) cc_final: 0.8385 (ptm-80) REVERT: W 28 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7902 (mm-40) REVERT: W 39 ARG cc_start: 0.7961 (ttm-80) cc_final: 0.7674 (tmm160) REVERT: W 105 GLU cc_start: 0.7233 (tt0) cc_final: 0.7001 (tt0) outliers start: 13 outliers final: 11 residues processed: 147 average time/residue: 0.3976 time to fit residues: 72.6978 Evaluate side-chains 153 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 1.388 ------------------------------------------------------------------------------- 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 W residue 50 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 0.0020 chunk 116 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- 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 28 GLN S 59 GLN S 80 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2447 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 : 0.394 4.506 14520 Z= 0.206 Chirality : 0.036 0.114 1572 Planarity : 0.003 0.025 1884 Dihedral : 3.373 9.649 1452 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 1.13 % Allowed : 7.99 % Favored : 90.89 % 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: 1.33 (0.23), residues: 1284 helix: 2.19 (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 0.001 TRP C 16 HIS 0.002 0.001 HIS C 89 PHE 0.004 0.001 PHE D 16 TYR 0.005 0.001 TYR A 29 ARG 0.004 0.000 ARG Q 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 155 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 1.285 Fit side-chains REVERT: C 43 ARG cc_start: 0.7189 (mmt-90) cc_final: 0.5940 (ptm-80) REVERT: E 39 ARG cc_start: 0.8144 (ttm-80) cc_final: 0.7801 (ttm110) REVERT: E 40 GLU cc_start: 0.7832 (tp30) cc_final: 0.7584 (tp30) REVERT: E 43 ARG cc_start: 0.7049 (mmt-90) cc_final: 0.5660 (ptm-80) REVERT: G 90 GLN cc_start: 0.7520 (mm110) cc_final: 0.7172 (mm110) REVERT: K 28 GLN cc_start: 0.8403 (mm-40) cc_final: 0.8032 (mm-40) REVERT: K 39 ARG cc_start: 0.8034 (ttm-80) cc_final: 0.7632 (ttm170) REVERT: K 43 ARG cc_start: 0.7130 (mmt-90) cc_final: 0.5960 (ptm-80) REVERT: M 43 ARG cc_start: 0.7151 (mmt-90) cc_final: 0.6005 (ptm160) REVERT: O 28 GLN cc_start: 0.8265 (mm-40) cc_final: 0.8054 (mm-40) REVERT: O 39 ARG cc_start: 0.8158 (ttm-80) cc_final: 0.7811 (ttp-170) REVERT: O 43 ARG cc_start: 0.7221 (mmt-90) cc_final: 0.6498 (mtp-110) REVERT: S 39 ARG cc_start: 0.8031 (ttm-80) cc_final: 0.7552 (ttm170) REVERT: S 43 ARG cc_start: 0.7160 (mmt-90) cc_final: 0.6325 (ttp80) REVERT: T 12 ARG cc_start: 0.8687 (ptm-80) cc_final: 0.8411 (ptm-80) REVERT: W 28 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7881 (mm-40) REVERT: W 39 ARG cc_start: 0.7968 (ttm-80) cc_final: 0.7647 (ttp-170) REVERT: W 105 GLU cc_start: 0.7314 (tt0) cc_final: 0.7073 (tt0) outliers start: 13 outliers final: 12 residues processed: 142 average time/residue: 0.4125 time to fit residues: 73.0822 Evaluate side-chains 153 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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 M residue 95 LYS Chi-restraints excluded: chain O residue 46 VAL 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 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 111 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 59 GLN S 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2570 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= 0.174 Angle : 0.391 4.803 14520 Z= 0.204 Chirality : 0.036 0.114 1572 Planarity : 0.003 0.025 1884 Dihedral : 3.330 9.145 1452 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 1.39 % Allowed : 8.33 % 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 (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: 2.25 (0.19), residues: 840 sheet: None (None), residues: 0 loop : -1.85 (0.18), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 16 HIS 0.002 0.001 HIS C 89 PHE 0.004 0.001 PHE D 16 TYR 0.004 0.001 TYR E 79 ARG 0.008 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 160 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 1.243 Fit side-chains REVERT: C 43 ARG cc_start: 0.7154 (mmt-90) cc_final: 0.5781 (ptm-80) REVERT: E 39 ARG cc_start: 0.8167 (ttm-80) cc_final: 0.7809 (ttm110) REVERT: E 43 ARG cc_start: 0.7044 (mmt-90) cc_final: 0.5760 (ptm-80) REVERT: K 28 GLN cc_start: 0.8361 (mm-40) cc_final: 0.8001 (mm-40) REVERT: K 39 ARG cc_start: 0.7999 (ttm-80) cc_final: 0.7604 (ttm170) REVERT: K 43 ARG cc_start: 0.7172 (mmt-90) cc_final: 0.5981 (ptm-80) REVERT: M 43 ARG cc_start: 0.7155 (mmt-90) cc_final: 0.6002 (ptm160) REVERT: O 28 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7978 (mm-40) REVERT: O 39 ARG cc_start: 0.8163 (ttm-80) cc_final: 0.7819 (ttp-170) REVERT: O 43 ARG cc_start: 0.7132 (mmt-90) cc_final: 0.6449 (mtp-110) REVERT: S 39 ARG cc_start: 0.8053 (ttm-80) cc_final: 0.7615 (ttm170) REVERT: T 12 ARG cc_start: 0.8697 (ptm-80) cc_final: 0.8447 (ptm-80) REVERT: W 28 GLN cc_start: 0.8234 (mm-40) cc_final: 0.7865 (mm-40) REVERT: W 39 ARG cc_start: 0.7972 (ttm-80) cc_final: 0.7634 (ttp-170) REVERT: W 105 GLU cc_start: 0.7316 (tt0) cc_final: 0.7099 (tt0) outliers start: 16 outliers final: 13 residues processed: 149 average time/residue: 0.3989 time to fit residues: 74.2847 Evaluate side-chains 154 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 1.293 ------------------------------------------------------------------------------- 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 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 20 ARG 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 71 optimal weight: 0.2980 chunk 46 optimal weight: 0.0770 chunk 69 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 GLN ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN S 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 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 : 0.003 0.024 10824 Z= 0.186 Angle : 0.405 4.757 14520 Z= 0.209 Chirality : 0.036 0.116 1572 Planarity : 0.003 0.033 1884 Dihedral : 3.346 9.389 1452 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 1.82 % Allowed : 8.68 % Favored : 89.50 % 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: 2.25 (0.19), residues: 840 sheet: None (None), residues: 0 loop : -1.87 (0.18), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 16 HIS 0.002 0.001 HIS G 33 PHE 0.004 0.001 PHE P 16 TYR 0.007 0.001 TYR C 29 ARG 0.007 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 162 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 1.281 Fit side-chains REVERT: C 43 ARG cc_start: 0.7177 (mmt-90) cc_final: 0.5800 (ptm-80) REVERT: E 39 ARG cc_start: 0.8174 (ttm-80) cc_final: 0.7852 (ttm110) REVERT: I 105 GLU cc_start: 0.7326 (tt0) cc_final: 0.7069 (tt0) REVERT: K 28 GLN cc_start: 0.8396 (mm-40) cc_final: 0.7994 (mm-40) REVERT: K 39 ARG cc_start: 0.8009 (ttm-80) cc_final: 0.7606 (ttm170) REVERT: K 43 ARG cc_start: 0.7185 (mmt-90) cc_final: 0.5993 (ptm-80) REVERT: M 43 ARG cc_start: 0.7178 (mmt-90) cc_final: 0.5978 (ptm160) REVERT: O 28 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7970 (mm-40) REVERT: O 39 ARG cc_start: 0.8161 (ttm-80) cc_final: 0.7819 (ttp-170) REVERT: O 43 ARG cc_start: 0.7146 (mmt-90) cc_final: 0.6442 (mtp-110) REVERT: Q 17 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7605 (mt-10) REVERT: Q 69 GLN cc_start: 0.8666 (tp40) cc_final: 0.8442 (tt0) REVERT: S 39 ARG cc_start: 0.8051 (ttm-80) cc_final: 0.7613 (ttm170) REVERT: T 12 ARG cc_start: 0.8691 (ptm-80) cc_final: 0.8451 (ptm-80) REVERT: W 28 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7858 (mm-40) REVERT: W 39 ARG cc_start: 0.7971 (ttm-80) cc_final: 0.7629 (ttp-170) REVERT: W 105 GLU cc_start: 0.7321 (tt0) cc_final: 0.7113 (tt0) outliers start: 21 outliers final: 15 residues processed: 147 average time/residue: 0.3827 time to fit residues: 71.2905 Evaluate side-chains 158 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 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 20 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 46 optimal weight: 0.3980 chunk 84 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 113 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 GLN ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 GLN S 80 ASN ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2659 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= 0.168 Angle : 0.397 4.527 14520 Z= 0.205 Chirality : 0.036 0.113 1572 Planarity : 0.003 0.029 1884 Dihedral : 3.280 10.051 1452 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.22 % Allowed : 9.29 % Favored : 89.50 % 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: 1.43 (0.23), residues: 1284 helix: 2.29 (0.19), residues: 840 sheet: None (None), residues: 0 loop : -1.84 (0.19), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 16 HIS 0.002 0.001 HIS C 89 PHE 0.004 0.001 PHE D 16 TYR 0.006 0.001 TYR C 29 ARG 0.007 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 156 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 1.136 Fit side-chains REVERT: C 43 ARG cc_start: 0.7144 (mmt-90) cc_final: 0.5762 (ptm-80) REVERT: E 39 ARG cc_start: 0.8177 (ttm-80) cc_final: 0.7812 (ttm110) REVERT: E 43 ARG cc_start: 0.6990 (mmt-90) cc_final: 0.5718 (ptm-80) REVERT: I 39 ARG cc_start: 0.8350 (ttp-170) cc_final: 0.8113 (ttp-170) REVERT: I 105 GLU cc_start: 0.7316 (tt0) cc_final: 0.7072 (tt0) REVERT: K 28 GLN cc_start: 0.8378 (mm-40) cc_final: 0.8000 (mm-40) REVERT: K 39 ARG cc_start: 0.8016 (ttm-80) cc_final: 0.7615 (ttm170) REVERT: K 43 ARG cc_start: 0.7163 (mmt-90) cc_final: 0.6453 (mtp-110) REVERT: M 43 ARG cc_start: 0.7206 (mmt-90) cc_final: 0.5995 (ptm160) REVERT: O 39 ARG cc_start: 0.8168 (ttm-80) cc_final: 0.7825 (ttp-170) REVERT: O 43 ARG cc_start: 0.7111 (mmt-90) cc_final: 0.6425 (mtp-110) REVERT: Q 17 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7607 (mt-10) REVERT: Q 69 GLN cc_start: 0.8666 (tp40) cc_final: 0.8441 (tt0) REVERT: S 39 ARG cc_start: 0.8054 (ttm-80) cc_final: 0.7616 (ttm170) REVERT: T 12 ARG cc_start: 0.8693 (ptm-80) cc_final: 0.8455 (ptm-80) REVERT: W 28 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7863 (mm-40) REVERT: W 39 ARG cc_start: 0.7968 (ttm-80) cc_final: 0.7631 (ttp-170) REVERT: W 105 GLU cc_start: 0.7322 (tt0) cc_final: 0.7115 (tt0) outliers start: 14 outliers final: 14 residues processed: 145 average time/residue: 0.3978 time to fit residues: 72.7289 Evaluate side-chains 156 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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 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 20 ARG 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 54 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 119 optimal weight: 0.4980 chunk 110 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 29 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: ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 GLN ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN S 80 ASN ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2704 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 : 0.406 4.520 14520 Z= 0.209 Chirality : 0.036 0.115 1572 Planarity : 0.003 0.030 1884 Dihedral : 3.325 10.386 1452 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.39 % Allowed : 9.46 % Favored : 89.15 % 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: 1.39 (0.23), residues: 1284 helix: 2.27 (0.19), residues: 840 sheet: None (None), residues: 0 loop : -1.87 (0.18), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 16 HIS 0.002 0.001 HIS G 33 PHE 0.005 0.001 PHE D 16 TYR 0.006 0.001 TYR C 29 ARG 0.007 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 152 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 1.238 Fit side-chains REVERT: C 43 ARG cc_start: 0.7162 (mmt-90) cc_final: 0.5768 (ptm-80) REVERT: E 39 ARG cc_start: 0.8175 (ttm-80) cc_final: 0.7853 (ttm110) REVERT: I 39 ARG cc_start: 0.8363 (ttp-170) cc_final: 0.8110 (ttp-170) REVERT: I 105 GLU cc_start: 0.7324 (tt0) cc_final: 0.7076 (tt0) REVERT: K 28 GLN cc_start: 0.8375 (mm-40) cc_final: 0.7995 (mm-40) REVERT: K 39 ARG cc_start: 0.8011 (ttm-80) cc_final: 0.7609 (ttm170) REVERT: K 43 ARG cc_start: 0.7185 (mmt-90) cc_final: 0.5990 (ptm-80) REVERT: M 43 ARG cc_start: 0.7230 (mmt-90) cc_final: 0.6000 (ptm160) REVERT: O 28 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7992 (mm-40) REVERT: O 39 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7822 (ttp-170) REVERT: O 43 ARG cc_start: 0.7057 (mmt-90) cc_final: 0.6378 (mtp-110) REVERT: Q 17 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7610 (mt-10) REVERT: Q 69 GLN cc_start: 0.8663 (tp40) cc_final: 0.8444 (tt0) REVERT: S 39 ARG cc_start: 0.8053 (ttm-80) cc_final: 0.7614 (ttm170) REVERT: W 28 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7882 (mm-40) REVERT: W 39 ARG cc_start: 0.7944 (ttm-80) cc_final: 0.7639 (ttp-170) REVERT: W 105 GLU cc_start: 0.7353 (tt0) cc_final: 0.7137 (tt0) outliers start: 16 outliers final: 15 residues processed: 140 average time/residue: 0.4040 time to fit residues: 71.7437 Evaluate side-chains 152 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 1.288 ------------------------------------------------------------------------------- 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 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 20 ARG 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 87 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.0030 chunk 95 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 68 optimal weight: 0.2980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 GLN ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 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 = 0.3749 r_free = 0.3749 target = 0.156799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.118959 restraints weight = 10031.475| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.54 r_work: 0.3138 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.300 10824 Z= 0.263 Angle : 0.831 58.987 14520 Z= 0.469 Chirality : 0.036 0.115 1572 Planarity : 0.003 0.028 1884 Dihedral : 3.319 10.409 1452 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.30 % Allowed : 9.38 % Favored : 89.32 % 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: 1.39 (0.23), residues: 1284 helix: 2.27 (0.19), residues: 840 sheet: None (None), residues: 0 loop : -1.87 (0.18), 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 0.005 0.000 ARG U 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2598.33 seconds wall clock time: 48 minutes 51.23 seconds (2931.23 seconds total)