Starting phenix.real_space_refine on Mon Jul 28 14:45:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h1p_51769/07_2025/9h1p_51769.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h1p_51769/07_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_51769/07_2025/9h1p_51769.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h1p_51769/07_2025/9h1p_51769.map" model { file = "/net/cci-nas-00/data/ceres_data/9h1p_51769/07_2025/9h1p_51769.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h1p_51769/07_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-5711/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: 5.00, per 1000 atoms: 0.47 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: 2.52 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: 0.93 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: 2.58 Time building geometry restraints manager: 2.98 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: 11.210 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 23.670 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10824 Z= 0.171 Angle : 0.669 4.701 14520 Z= 0.402 Chirality : 0.045 0.119 1572 Planarity : 0.010 0.095 1884 Dihedral : 13.913 72.187 4236 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.11971 ( 552) hydrogen bonds : angle 3.88040 ( 1548) covalent geometry : bond 0.00364 (10824) covalent geometry : angle 0.66885 (14520) *********************** 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 : 1.211 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: 0.4572 time to fit residues: 98.6535 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 : 1.208 ------------------------------------------------------------------------------- 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 = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.127134 restraints weight = 9773.329| |-----------------------------------------------------------------------------| 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= 0.214 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 Details of bonding type rmsd hydrogen bonds : bond 0.05930 ( 552) hydrogen bonds : angle 3.52818 ( 1548) covalent geometry : bond 0.00544 (10824) covalent geometry : angle 0.57996 (14520) *********************** 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 : 1.270 Fit side-chains REVERT: C 43 ARG cc_start: 0.7306 (mmt-90) cc_final: 0.5719 (ptm-80) REVERT: E 39 ARG cc_start: 0.7466 (ttm-80) cc_final: 0.7173 (ttm110) REVERT: E 40 GLU cc_start: 0.7623 (tp30) cc_final: 0.7100 (tp30) REVERT: E 43 ARG cc_start: 0.7207 (mmt-90) cc_final: 0.5527 (ptm-80) REVERT: G 90 GLN cc_start: 0.6966 (mm110) cc_final: 0.6707 (mm110) REVERT: I 39 ARG cc_start: 0.7442 (ttm-80) cc_final: 0.7153 (ttp-170) REVERT: K 39 ARG cc_start: 0.7225 (ttm-80) cc_final: 0.6817 (ttp-170) REVERT: K 40 GLU cc_start: 0.7489 (tp30) cc_final: 0.7244 (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: 0.7430 (ttm-80) cc_final: 0.7008 (ttp-170) REVERT: O 43 ARG cc_start: 0.7470 (mmt-90) cc_final: 0.6087 (mtp-110) REVERT: Q 90 GLN cc_start: 0.7034 (mm110) cc_final: 0.6827 (mm110) REVERT: S 39 ARG cc_start: 0.7249 (ttm-80) cc_final: 0.6733 (ttm170) REVERT: W 39 ARG cc_start: 0.7488 (ttm-80) cc_final: 0.6885 (tmm160) REVERT: W 105 GLU cc_start: 0.7211 (tt0) cc_final: 0.6948 (tt0) outliers start: 2 outliers final: 1 residues processed: 147 average time/residue: 0.3890 time to fit residues: 71.7160 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 : 1.278 ------------------------------------------------------------------------------- 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: 0.9990 chunk 13 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 0.3980 chunk 7 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 111 optimal weight: 0.0070 chunk 5 optimal weight: 0.8980 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 = 0.3877 r_free = 0.3877 target = 0.164375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.128206 restraints weight = 9854.378| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.44 r_work: 0.3282 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.1885 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= 0.095 Angle : 0.398 4.549 14520 Z= 0.214 Chirality : 0.036 0.118 1572 Planarity : 0.004 0.030 1884 Dihedral : 3.725 11.466 1452 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.69 % Allowed : 4.95 % 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: 0.85 (0.22), residues: 1284 helix: 1.59 (0.19), residues: 852 sheet: None (None), residues: 0 loop : -1.57 (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 S 89 PHE 0.003 0.000 PHE F 16 TYR 0.007 0.001 TYR A 29 ARG 0.006 0.000 ARG Q 39 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 552) hydrogen bonds : angle 3.06951 ( 1548) covalent geometry : bond 0.00219 (10824) covalent geometry : angle 0.39763 (14520) *********************** 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: 8 poor density : 157 time to evaluate : 1.409 Fit side-chains REVERT: A 40 GLU cc_start: 0.7763 (tp30) cc_final: 0.7492 (tp30) REVERT: A 43 ARG cc_start: 0.7109 (mmt-90) cc_final: 0.5395 (ptm-80) REVERT: C 43 ARG cc_start: 0.7115 (mmt-90) cc_final: 0.5539 (ptm-80) REVERT: E 39 ARG cc_start: 0.7534 (ttm-80) cc_final: 0.7220 (ttm110) REVERT: E 40 GLU cc_start: 0.7500 (tp30) cc_final: 0.7059 (tp30) REVERT: E 43 ARG cc_start: 0.7163 (mmt-90) cc_final: 0.5425 (ptm-80) REVERT: G 43 ARG cc_start: 0.7022 (mmt-90) cc_final: 0.5606 (ttp80) REVERT: G 90 GLN cc_start: 0.6763 (mm110) cc_final: 0.6480 (mm110) REVERT: I 39 ARG cc_start: 0.7509 (ttm-80) cc_final: 0.7157 (ttp-170) REVERT: I 43 ARG cc_start: 0.7124 (mmt-90) cc_final: 0.5406 (ptm160) REVERT: K 39 ARG cc_start: 0.7307 (ttm-80) cc_final: 0.6886 (ttp-170) REVERT: K 43 ARG cc_start: 0.7096 (mmt-90) cc_final: 0.5952 (mtp-110) REVERT: M 43 ARG cc_start: 0.7100 (mmt-90) cc_final: 0.5740 (ttp80) REVERT: O 39 ARG cc_start: 0.7576 (ttm-80) cc_final: 0.7102 (ttp-170) REVERT: O 43 ARG cc_start: 0.7305 (mmt-90) cc_final: 0.6084 (mtp-110) REVERT: Q 43 ARG cc_start: 0.7066 (mmt-90) cc_final: 0.5262 (ptm-80) REVERT: Q 90 GLN cc_start: 0.6920 (mm110) cc_final: 0.6684 (mm110) REVERT: S 39 ARG cc_start: 0.7361 (ttm-80) cc_final: 0.6895 (ttm170) REVERT: S 43 ARG cc_start: 0.7263 (mmt-90) cc_final: 0.5893 (ttp80) REVERT: U 43 ARG cc_start: 0.7084 (mmt-90) cc_final: 0.5532 (ttp80) REVERT: W 28 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7624 (mm-40) REVERT: W 39 ARG cc_start: 0.7440 (ttm-80) cc_final: 0.6945 (ttp-170) REVERT: W 43 ARG cc_start: 0.6937 (mmt-90) cc_final: 0.5608 (ttp80) REVERT: W 105 GLU cc_start: 0.7272 (tt0) cc_final: 0.7023 (tt0) outliers start: 8 outliers final: 5 residues processed: 158 average time/residue: 0.4052 time to fit residues: 79.5045 Evaluate side-chains 152 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 147 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 79 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 80 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.158510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.120370 restraints weight = 10105.637| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.57 r_work: 0.3162 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.2117 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= 0.127 Angle : 0.428 4.590 14520 Z= 0.225 Chirality : 0.037 0.117 1572 Planarity : 0.004 0.026 1884 Dihedral : 3.676 11.284 1452 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.95 % Allowed : 5.99 % Favored : 93.06 % 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: 1.08 (0.23), residues: 1284 helix: 1.86 (0.19), residues: 852 sheet: None (None), residues: 0 loop : -1.72 (0.19), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 552) hydrogen bonds : angle 3.11662 ( 1548) covalent geometry : bond 0.00317 (10824) covalent geometry : angle 0.42776 (14520) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 1.629 Fit side-chains REVERT: A 40 GLU cc_start: 0.7726 (tp30) cc_final: 0.7503 (tp30) REVERT: C 43 ARG cc_start: 0.7312 (mmt-90) cc_final: 0.5700 (ptm-80) REVERT: E 39 ARG cc_start: 0.7721 (ttm-80) cc_final: 0.7397 (ttm110) REVERT: E 40 GLU cc_start: 0.7553 (tp30) cc_final: 0.7150 (tp30) REVERT: E 43 ARG cc_start: 0.7177 (mmt-90) cc_final: 0.5238 (ptm-80) REVERT: E 105 GLU cc_start: 0.7184 (tt0) cc_final: 0.6975 (tt0) REVERT: G 90 GLN cc_start: 0.6956 (mm110) cc_final: 0.6685 (mm110) REVERT: I 39 ARG cc_start: 0.7537 (ttm-80) cc_final: 0.7134 (ttp-170) REVERT: K 28 GLN cc_start: 0.8289 (mm-40) cc_final: 0.7840 (mm-40) REVERT: K 39 ARG cc_start: 0.7470 (ttm-80) cc_final: 0.6997 (ttm170) REVERT: K 43 ARG cc_start: 0.7209 (mmt-90) cc_final: 0.6052 (mtp-110) REVERT: M 43 ARG cc_start: 0.7171 (mmt-90) cc_final: 0.5662 (ptm-80) REVERT: O 39 ARG cc_start: 0.7724 (ttm-80) cc_final: 0.7262 (ttp-170) REVERT: O 43 ARG cc_start: 0.7389 (mmt-90) cc_final: 0.6041 (mtp-110) REVERT: Q 90 GLN cc_start: 0.7015 (mm110) cc_final: 0.6774 (mm110) REVERT: S 39 ARG cc_start: 0.7429 (ttm-80) cc_final: 0.6901 (ttm170) REVERT: S 43 ARG cc_start: 0.7357 (mmt-90) cc_final: 0.6077 (ttp80) REVERT: W 39 ARG cc_start: 0.7447 (ttm-80) cc_final: 0.6890 (ttp-170) REVERT: W 105 GLU cc_start: 0.7264 (tt0) cc_final: 0.6989 (tt0) outliers start: 11 outliers final: 9 residues processed: 142 average time/residue: 0.3864 time to fit residues: 69.1434 Evaluate side-chains 149 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 38 SER Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain Q residue 20 ARG 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: 0.0010 chunk 54 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 59 GLN ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN S 28 GLN S 59 GLN S 80 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.159360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.122159 restraints weight = 9970.213| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.49 r_work: 0.3216 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2288 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= 0.102 Angle : 0.386 4.538 14520 Z= 0.203 Chirality : 0.036 0.115 1572 Planarity : 0.003 0.025 1884 Dihedral : 3.379 9.966 1452 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.95 % Allowed : 6.77 % Favored : 92.27 % 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: 2.03 (0.19), residues: 852 sheet: None (None), residues: 0 loop : -1.69 (0.19), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 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 0.006 0.000 ARG G 39 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 552) hydrogen bonds : angle 2.97458 ( 1548) covalent geometry : bond 0.00246 (10824) covalent geometry : angle 0.38639 (14520) *********************** 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 158 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 1.222 Fit side-chains REVERT: A 40 GLU cc_start: 0.7671 (tp30) cc_final: 0.7420 (tp30) REVERT: A 43 ARG cc_start: 0.7153 (mmt-90) cc_final: 0.5365 (ptm-80) REVERT: C 43 ARG cc_start: 0.7190 (mmt-90) cc_final: 0.5549 (ptm-80) REVERT: E 39 ARG cc_start: 0.7789 (ttm-80) cc_final: 0.7457 (ttm110) REVERT: E 40 GLU cc_start: 0.7624 (tp30) cc_final: 0.7278 (tp30) REVERT: E 43 ARG cc_start: 0.7155 (mmt-90) cc_final: 0.5305 (ptm-80) REVERT: E 105 GLU cc_start: 0.7221 (tt0) cc_final: 0.7017 (tt0) REVERT: G 90 GLN cc_start: 0.6967 (mm110) cc_final: 0.6674 (mm110) REVERT: I 39 ARG cc_start: 0.7559 (ttm-80) cc_final: 0.7212 (ttp-170) REVERT: I 43 ARG cc_start: 0.7137 (mmt-90) cc_final: 0.5395 (ptm160) REVERT: K 28 GLN cc_start: 0.8282 (mm-40) cc_final: 0.7794 (mm-40) REVERT: K 39 ARG cc_start: 0.7525 (ttm-80) cc_final: 0.7023 (ttm170) REVERT: K 43 ARG cc_start: 0.7193 (mmt-90) cc_final: 0.5867 (mtp-110) REVERT: M 43 ARG cc_start: 0.7185 (mmt-90) cc_final: 0.5691 (ptm160) REVERT: O 39 ARG cc_start: 0.7779 (ttm-80) cc_final: 0.7309 (ttp-170) REVERT: O 43 ARG cc_start: 0.7325 (mmt-90) cc_final: 0.6089 (mtp-110) REVERT: S 39 ARG cc_start: 0.7507 (ttm-80) cc_final: 0.6937 (ttm170) REVERT: S 43 ARG cc_start: 0.7327 (mmt-90) cc_final: 0.6007 (ttp80) REVERT: T 12 ARG cc_start: 0.8284 (ptm-80) cc_final: 0.8059 (ptm-80) REVERT: W 28 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7696 (mm-40) REVERT: W 39 ARG cc_start: 0.7480 (ttm-80) cc_final: 0.6927 (tmm160) REVERT: W 105 GLU cc_start: 0.7265 (tt0) cc_final: 0.7011 (tt0) outliers start: 11 outliers final: 7 residues processed: 148 average time/residue: 0.4004 time to fit residues: 73.8409 Evaluate side-chains 153 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Q residue 95 LYS Chi-restraints excluded: chain S residue 20 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 41 optimal weight: 0.0270 chunk 6 optimal weight: 0.0170 chunk 69 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 108 optimal weight: 0.0470 chunk 115 optimal weight: 0.3980 chunk 44 optimal weight: 0.0470 chunk 71 optimal weight: 0.6980 overall best weight: 0.1072 ------------------------------------------------------------------------------- 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 O 28 GLN S 28 GLN S 59 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.166736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.130761 restraints weight = 9855.233| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.44 r_work: 0.3345 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.015 10824 Z= 0.065 Angle : 0.335 4.442 14520 Z= 0.174 Chirality : 0.035 0.116 1572 Planarity : 0.003 0.025 1884 Dihedral : 2.847 8.410 1452 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.95 % Allowed : 7.38 % Favored : 91.67 % 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: 1.75 (0.24), residues: 1284 helix: 2.37 (0.19), residues: 852 sheet: None (None), residues: 0 loop : -1.44 (0.20), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 16 HIS 0.000 0.000 HIS O 89 PHE 0.002 0.000 PHE N 16 TYR 0.004 0.001 TYR M 86 ARG 0.006 0.000 ARG G 39 Details of bonding type rmsd hydrogen bonds : bond 0.02425 ( 552) hydrogen bonds : angle 2.68400 ( 1548) covalent geometry : bond 0.00128 (10824) covalent geometry : angle 0.33493 (14520) *********************** 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: 11 poor density : 163 time to evaluate : 1.207 Fit side-chains REVERT: A 43 ARG cc_start: 0.6838 (mmt-90) cc_final: 0.5272 (ptm-80) REVERT: C 43 ARG cc_start: 0.6919 (mmt-90) cc_final: 0.5337 (ptm-80) REVERT: E 39 ARG cc_start: 0.7770 (ttm-80) cc_final: 0.7390 (ttm110) REVERT: E 43 ARG cc_start: 0.6987 (mmt-90) cc_final: 0.5229 (ptm-80) REVERT: G 43 ARG cc_start: 0.7053 (mmt-90) cc_final: 0.5711 (ttp80) REVERT: I 20 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7392 (ptp-170) REVERT: I 39 ARG cc_start: 0.7542 (ttm-80) cc_final: 0.7155 (ttp-170) REVERT: I 43 ARG cc_start: 0.6988 (mmt-90) cc_final: 0.5307 (ptm160) REVERT: K 28 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7657 (mm-40) REVERT: K 39 ARG cc_start: 0.7551 (ttm-80) cc_final: 0.7039 (ttm170) REVERT: K 43 ARG cc_start: 0.7088 (mmt-90) cc_final: 0.5900 (mtp-110) REVERT: L 12 ARG cc_start: 0.8188 (ptm-80) cc_final: 0.7851 (ttp80) REVERT: M 43 ARG cc_start: 0.7023 (mmt-90) cc_final: 0.5726 (ttp80) REVERT: O 39 ARG cc_start: 0.7779 (ttm-80) cc_final: 0.7290 (ttp-170) REVERT: O 43 ARG cc_start: 0.7171 (mmt-90) cc_final: 0.5860 (ttp80) REVERT: Q 43 ARG cc_start: 0.7041 (mmt-90) cc_final: 0.5693 (ttp80) REVERT: S 39 ARG cc_start: 0.7478 (ttm-80) cc_final: 0.6934 (ttm170) REVERT: S 43 ARG cc_start: 0.7043 (mmt-90) cc_final: 0.5834 (ttp80) REVERT: T 12 ARG cc_start: 0.8192 (ptm-80) cc_final: 0.7841 (ttp80) REVERT: U 43 ARG cc_start: 0.6927 (mmt-90) cc_final: 0.5424 (ttp80) REVERT: W 28 GLN cc_start: 0.7921 (mm-40) cc_final: 0.7548 (mm-40) REVERT: W 39 ARG cc_start: 0.7459 (ttm-80) cc_final: 0.6971 (tmm160) REVERT: W 43 ARG cc_start: 0.6800 (mmt-90) cc_final: 0.5579 (ttp80) REVERT: W 105 GLU cc_start: 0.7311 (tt0) cc_final: 0.7055 (tt0) outliers start: 11 outliers final: 7 residues processed: 164 average time/residue: 0.4380 time to fit residues: 88.9832 Evaluate side-chains 157 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain I residue 20 ARG 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 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: 0.0980 chunk 35 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 58 optimal weight: 0.0060 chunk 64 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 104 optimal weight: 0.0040 overall best weight: 0.3208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 28 GLN S 80 ASN ** 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 = 0.3835 r_free = 0.3835 target = 0.163407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.126156 restraints weight = 10202.054| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.52 r_work: 0.3283 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2616 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= 0.075 Angle : 0.347 4.629 14520 Z= 0.180 Chirality : 0.035 0.113 1572 Planarity : 0.003 0.029 1884 Dihedral : 2.871 8.082 1452 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.69 % Allowed : 8.33 % Favored : 90.97 % 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: 1.84 (0.24), residues: 1284 helix: 2.44 (0.19), residues: 852 sheet: None (None), residues: 0 loop : -1.41 (0.20), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 16 HIS 0.001 0.000 HIS W 33 PHE 0.003 0.000 PHE X 16 TYR 0.005 0.001 TYR M 86 ARG 0.007 0.000 ARG G 39 Details of bonding type rmsd hydrogen bonds : bond 0.02915 ( 552) hydrogen bonds : angle 2.69236 ( 1548) covalent geometry : bond 0.00165 (10824) covalent geometry : angle 0.34683 (14520) *********************** 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 159 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: A 43 ARG cc_start: 0.6962 (mmt-90) cc_final: 0.5248 (ptm-80) REVERT: C 43 ARG cc_start: 0.7018 (mmt-90) cc_final: 0.5352 (ptm-80) REVERT: E 39 ARG cc_start: 0.7733 (ttm-80) cc_final: 0.7364 (ttm110) REVERT: E 43 ARG cc_start: 0.7055 (mmt-90) cc_final: 0.5218 (ptm-80) REVERT: I 43 ARG cc_start: 0.7001 (mmt-90) cc_final: 0.5280 (ptm160) REVERT: K 28 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7663 (mm-40) REVERT: K 39 ARG cc_start: 0.7482 (ttm-80) cc_final: 0.7001 (ttm170) REVERT: K 43 ARG cc_start: 0.7169 (mmt-90) cc_final: 0.5894 (mtp-110) REVERT: L 12 ARG cc_start: 0.8177 (ptm-80) cc_final: 0.7790 (ttp80) REVERT: M 43 ARG cc_start: 0.7045 (mmt-90) cc_final: 0.5410 (ptm160) REVERT: O 28 GLN cc_start: 0.8084 (mm110) cc_final: 0.7871 (mm-40) REVERT: O 39 ARG cc_start: 0.7738 (ttm-80) cc_final: 0.7239 (ttp-170) REVERT: O 43 ARG cc_start: 0.7182 (mmt-90) cc_final: 0.5969 (mtp-110) REVERT: Q 43 ARG cc_start: 0.7048 (mmt-90) cc_final: 0.5371 (ptm-80) REVERT: S 39 ARG cc_start: 0.7451 (ttm-80) cc_final: 0.6883 (ttm170) REVERT: S 43 ARG cc_start: 0.7190 (mmt-90) cc_final: 0.5808 (ttp80) REVERT: T 12 ARG cc_start: 0.8182 (ptm-80) cc_final: 0.7777 (ttp80) REVERT: U 43 ARG cc_start: 0.7016 (mmt-90) cc_final: 0.5433 (ttp80) REVERT: W 28 GLN cc_start: 0.7948 (mm-40) cc_final: 0.7581 (mm-40) REVERT: W 39 ARG cc_start: 0.7396 (ttm-80) cc_final: 0.6880 (ttp-170) REVERT: W 43 ARG cc_start: 0.6860 (mmt-90) cc_final: 0.5250 (ptm-80) REVERT: W 105 GLU cc_start: 0.7282 (tt0) cc_final: 0.7028 (tt0) outliers start: 8 outliers final: 8 residues processed: 151 average time/residue: 0.4120 time to fit residues: 76.3641 Evaluate side-chains 157 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 68 LEU Chi-restraints excluded: chain M residue 95 LYS Chi-restraints excluded: chain Q residue 95 LYS 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: 0.0370 chunk 97 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 66 optimal weight: 0.0770 chunk 90 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 28 GLN S 80 ASN ** 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 = 0.3939 r_free = 0.3939 target = 0.168145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.133013 restraints weight = 9773.132| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.34 r_work: 0.3218 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.2619 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= 0.086 Angle : 0.362 4.510 14520 Z= 0.188 Chirality : 0.035 0.112 1572 Planarity : 0.003 0.027 1884 Dihedral : 2.991 8.304 1452 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.95 % Allowed : 8.59 % 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: 1.80 (0.24), residues: 1284 helix: 2.42 (0.19), residues: 852 sheet: None (None), residues: 0 loop : -1.45 (0.20), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 16 HIS 0.001 0.001 HIS W 33 PHE 0.002 0.000 PHE D 16 TYR 0.004 0.001 TYR M 86 ARG 0.006 0.000 ARG G 39 Details of bonding type rmsd hydrogen bonds : bond 0.03175 ( 552) hydrogen bonds : angle 2.73412 ( 1548) covalent geometry : bond 0.00200 (10824) covalent geometry : angle 0.36189 (14520) *********************** 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 155 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 1.316 Fit side-chains revert: symmetry clash REVERT: A 43 ARG cc_start: 0.6990 (mmt-90) cc_final: 0.5238 (ptm-80) REVERT: C 43 ARG cc_start: 0.7073 (mmt-90) cc_final: 0.5308 (ptm-80) REVERT: E 39 ARG cc_start: 0.7700 (ttm-80) cc_final: 0.7332 (ttm110) REVERT: E 43 ARG cc_start: 0.7115 (mmt-90) cc_final: 0.5178 (ptm-80) REVERT: I 20 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7442 (ptp-170) REVERT: I 43 ARG cc_start: 0.7030 (mmt-90) cc_final: 0.5275 (ptm160) REVERT: K 28 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7730 (mm-40) REVERT: K 39 ARG cc_start: 0.7437 (ttm-80) cc_final: 0.6949 (ttm170) REVERT: K 43 ARG cc_start: 0.7187 (mmt-90) cc_final: 0.5874 (mtp-110) REVERT: M 43 ARG cc_start: 0.7064 (mmt-90) cc_final: 0.5566 (ptm160) REVERT: O 28 GLN cc_start: 0.8077 (mm110) cc_final: 0.7842 (mm-40) REVERT: O 39 ARG cc_start: 0.7690 (ttm-80) cc_final: 0.7191 (ttp-170) REVERT: O 43 ARG cc_start: 0.7186 (mmt-90) cc_final: 0.5975 (mtp-110) REVERT: S 39 ARG cc_start: 0.7483 (ttm-80) cc_final: 0.6876 (ttm170) REVERT: S 43 ARG cc_start: 0.7176 (mmt-90) cc_final: 0.5929 (ttp80) REVERT: T 12 ARG cc_start: 0.8171 (ptm-80) cc_final: 0.7937 (ptm-80) REVERT: W 28 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7586 (mm-40) REVERT: W 39 ARG cc_start: 0.7376 (ttm-80) cc_final: 0.6777 (ttp-170) REVERT: W 105 GLU cc_start: 0.7238 (tt0) cc_final: 0.6961 (tt0) outliers start: 11 outliers final: 9 residues processed: 146 average time/residue: 0.3941 time to fit residues: 71.3480 Evaluate side-chains 154 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 20 ARG 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 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: 1.9990 chunk 97 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 118 optimal weight: 0.0770 chunk 65 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 111 optimal weight: 0.3980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 90 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 = 0.3798 r_free = 0.3798 target = 0.159914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122427 restraints weight = 10128.138| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.50 r_work: 0.3212 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10824 Z= 0.098 Angle : 0.379 5.415 14520 Z= 0.197 Chirality : 0.036 0.111 1572 Planarity : 0.003 0.044 1884 Dihedral : 3.088 8.898 1452 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.04 % Allowed : 8.33 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.72 (0.24), residues: 1284 helix: 2.38 (0.19), residues: 852 sheet: None (None), residues: 0 loop : -1.52 (0.19), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP W 16 HIS 0.002 0.001 HIS E 33 PHE 0.003 0.001 PHE P 16 TYR 0.004 0.001 TYR A 29 ARG 0.009 0.000 ARG G 39 Details of bonding type rmsd hydrogen bonds : bond 0.03413 ( 552) hydrogen bonds : angle 2.77874 ( 1548) covalent geometry : bond 0.00236 (10824) covalent geometry : angle 0.37882 (14520) *********************** 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 157 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: A 43 ARG cc_start: 0.7051 (mmt-90) cc_final: 0.5281 (ptm-80) REVERT: C 43 ARG cc_start: 0.7129 (mmt-90) cc_final: 0.5408 (ptm-80) REVERT: E 39 ARG cc_start: 0.7795 (ttm-80) cc_final: 0.7437 (ttm110) REVERT: E 43 ARG cc_start: 0.7149 (mmt-90) cc_final: 0.5242 (ptm-80) REVERT: I 43 ARG cc_start: 0.7117 (mmt-90) cc_final: 0.5359 (ptm160) REVERT: K 28 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7705 (mm-40) REVERT: K 39 ARG cc_start: 0.7504 (ttm-80) cc_final: 0.7015 (ttm170) REVERT: K 43 ARG cc_start: 0.7256 (mmt-90) cc_final: 0.5376 (ptm-80) REVERT: M 43 ARG cc_start: 0.7136 (mmt-90) cc_final: 0.5640 (ptm160) REVERT: O 28 GLN cc_start: 0.8035 (mm110) cc_final: 0.7827 (mm-40) REVERT: O 39 ARG cc_start: 0.7764 (ttm-80) cc_final: 0.7262 (ttp-170) REVERT: O 43 ARG cc_start: 0.7266 (mmt-90) cc_final: 0.6045 (mtp-110) REVERT: S 39 ARG cc_start: 0.7543 (ttm-80) cc_final: 0.6942 (ttm170) REVERT: S 43 ARG cc_start: 0.7267 (mmt-90) cc_final: 0.5976 (ttp80) REVERT: T 12 ARG cc_start: 0.8239 (ptm-80) cc_final: 0.8017 (ptm-80) REVERT: W 28 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7693 (mm-40) REVERT: W 39 ARG cc_start: 0.7440 (ttm-80) cc_final: 0.6850 (ttp-170) REVERT: W 105 GLU cc_start: 0.7363 (tt0) cc_final: 0.7086 (tt0) outliers start: 12 outliers final: 9 residues processed: 148 average time/residue: 0.4038 time to fit residues: 74.3874 Evaluate side-chains 155 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 0.3980 chunk 93 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 106 optimal weight: 0.0870 chunk 110 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.3808 r_free = 0.3808 target = 0.160896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.123455 restraints weight = 10045.600| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.49 r_work: 0.3208 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10824 Z= 0.089 Angle : 0.370 5.506 14520 Z= 0.191 Chirality : 0.035 0.112 1572 Planarity : 0.003 0.036 1884 Dihedral : 3.013 9.095 1452 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 0.87 % Allowed : 8.25 % 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: 1.62 (0.24), residues: 1284 helix: 2.30 (0.19), residues: 864 sheet: None (None), residues: 0 loop : -1.69 (0.19), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 16 HIS 0.001 0.001 HIS W 33 PHE 0.003 0.000 PHE D 16 TYR 0.005 0.001 TYR C 29 ARG 0.009 0.000 ARG G 39 Details of bonding type rmsd hydrogen bonds : bond 0.03193 ( 552) hydrogen bonds : angle 2.72980 ( 1548) covalent geometry : bond 0.00209 (10824) covalent geometry : angle 0.37045 (14520) ********************** 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 159 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 1.292 Fit side-chains revert: symmetry clash REVERT: A 43 ARG cc_start: 0.6997 (mmt-90) cc_final: 0.5266 (ptm-80) REVERT: C 43 ARG cc_start: 0.7089 (mmt-90) cc_final: 0.5339 (ptm-80) REVERT: E 39 ARG cc_start: 0.7726 (ttm-80) cc_final: 0.7361 (ttm110) REVERT: E 43 ARG cc_start: 0.7070 (mmt-90) cc_final: 0.5200 (ptm-80) REVERT: I 43 ARG cc_start: 0.7068 (mmt-90) cc_final: 0.5304 (ptm160) REVERT: I 105 GLU cc_start: 0.7288 (tt0) cc_final: 0.7036 (tt0) REVERT: K 28 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7652 (mm-40) REVERT: K 39 ARG cc_start: 0.7458 (ttm-80) cc_final: 0.6971 (ttm170) REVERT: K 43 ARG cc_start: 0.7255 (mmt-90) cc_final: 0.5933 (mtp-110) REVERT: M 43 ARG cc_start: 0.7112 (mmt-90) cc_final: 0.5603 (ptm160) REVERT: O 28 GLN cc_start: 0.7997 (mm110) cc_final: 0.7790 (mm-40) REVERT: O 39 ARG cc_start: 0.7734 (ttm-80) cc_final: 0.7228 (ttp-170) REVERT: O 43 ARG cc_start: 0.7185 (mmt-90) cc_final: 0.5982 (mtp-110) REVERT: S 39 ARG cc_start: 0.7522 (ttm-80) cc_final: 0.6910 (ttm170) REVERT: S 43 ARG cc_start: 0.7226 (mmt-90) cc_final: 0.5938 (ttp80) REVERT: T 12 ARG cc_start: 0.8177 (ptm-80) cc_final: 0.7957 (ptm-80) REVERT: W 28 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7665 (mm-40) REVERT: W 39 ARG cc_start: 0.7418 (ttm-80) cc_final: 0.6811 (ttp-170) REVERT: W 105 GLU cc_start: 0.7347 (tt0) cc_final: 0.7076 (tt0) outliers start: 10 outliers final: 10 residues processed: 149 average time/residue: 0.4259 time to fit residues: 79.0940 Evaluate side-chains 158 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 31 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.159942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.121981 restraints weight = 10085.617| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.53 r_work: 0.3189 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.2717 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= 0.108 Angle : 0.393 5.372 14520 Z= 0.202 Chirality : 0.036 0.112 1572 Planarity : 0.003 0.034 1884 Dihedral : 3.151 9.727 1452 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 0.87 % Allowed : 8.42 % Favored : 90.71 % 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: 1.67 (0.24), residues: 1284 helix: 2.34 (0.19), residues: 852 sheet: None (None), residues: 0 loop : -1.57 (0.19), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 16 HIS 0.002 0.001 HIS C 89 PHE 0.004 0.001 PHE D 16 TYR 0.005 0.001 TYR C 29 ARG 0.009 0.000 ARG G 39 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 552) hydrogen bonds : angle 2.80946 ( 1548) covalent geometry : bond 0.00264 (10824) covalent geometry : angle 0.39307 (14520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6039.50 seconds wall clock time: 106 minutes 12.73 seconds (6372.73 seconds total)