Starting phenix.real_space_refine on Thu Sep 10 23:49:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ygg_72923/09_2026/9ygg_72923.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ygg_72923/09_2026/9ygg_72923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ygg_72923/09_2026/9ygg_72923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ygg_72923/09_2026/9ygg_72923.map" model { file = "/net/cci-nas-00/data/ceres_data/9ygg_72923/09_2026/9ygg_72923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ygg_72923/09_2026/9ygg_72923.cif" } resolution = 4.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.044 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 3478 2.51 5 N 936 2.21 5 O 1065 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5503 Number of models: 1 Model: "" Number of chains: 7 Chain: "G" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 187 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 6, 'TRANS': 19} Chain: "H" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 939 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 833 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "M" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 939 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "N" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 833 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "O" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 939 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "P" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 833 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Time building chain proxies: 1.75, per 1000 atoms: 0.32 Number of scatterers: 5503 At special positions: 0 Unit cell: (60.654, 94.657, 115.794, 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 1065 8.00 N 936 7.00 C 3478 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.05 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 206.2 milliseconds 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1276 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 16 sheets defined 6.8% alpha, 39.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'H' and resid 52A through 55 removed outlier: 4.065A pdb=" N SER H 55 " --> pdb=" O PHE H 52A" (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 52A through 55' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.552A pdb=" N THR H 87 " --> pdb=" O VAL H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.559A pdb=" N VAL L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 55 removed outlier: 3.659A pdb=" N SER M 55 " --> pdb=" O PHE M 52A" (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 64 Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.934A pdb=" N THR M 87 " --> pdb=" O VAL M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.561A pdb=" N VAL N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 87 removed outlier: 3.947A pdb=" N THR O 87 " --> pdb=" O VAL O 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.663A pdb=" N SER H 25 " --> pdb=" O LYS H 3 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL H 5 " --> pdb=" O GLU H 23 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE H 79 " --> pdb=" O SER H 70 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER H 70 " --> pdb=" O PHE H 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.159A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.693A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS L 50 " --> pdb=" O SER L 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.718A pdb=" N THR L 97 " --> pdb=" O GLU L 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.527A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.592A pdb=" N SER M 25 " --> pdb=" O LYS M 3 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS M 22 " --> pdb=" O VAL M 78 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL M 78 " --> pdb=" O CYS M 22 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR M 77 " --> pdb=" O ASP M 72 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER M 70 " --> pdb=" O PHE M 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.673A pdb=" N GLY M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL M 89 " --> pdb=" O GLN M 39 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN M 39 " --> pdb=" O VAL M 89 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL M 48 " --> pdb=" O TRP M 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 96 through 98 Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 5 removed outlier: 3.688A pdb=" N VAL N 19 " --> pdb=" O ILE N 75 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE N 75 " --> pdb=" O VAL N 19 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE N 21 " --> pdb=" O LEU N 73 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU N 73 " --> pdb=" O ILE N 21 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS N 23 " --> pdb=" O PHE N 71 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.721A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU N 47 " --> pdb=" O TRP N 35 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN N 37 " --> pdb=" O LYS N 45 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS N 50 " --> pdb=" O SER N 53 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 Processing sheet with id=AB3, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.681A pdb=" N CYS O 22 " --> pdb=" O VAL O 78 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL O 78 " --> pdb=" O CYS O 22 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR O 77 " --> pdb=" O ASP O 72 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE O 79 " --> pdb=" O SER O 70 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER O 70 " --> pdb=" O PHE O 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'O' and resid 55 through 59 removed outlier: 5.381A pdb=" N THR O 57 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ALA O 50 " --> pdb=" O THR O 57 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N TYR O 59 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N VAL O 48 " --> pdb=" O TYR O 59 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ALA O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N MET O 34 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR O 107 " --> pdb=" O TYR O 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'P' and resid 4 through 6 removed outlier: 3.684A pdb=" N THR P 5 " --> pdb=" O ARG P 24 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG P 24 " --> pdb=" O THR P 5 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL P 19 " --> pdb=" O ILE P 75 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER P 65 " --> pdb=" O THR P 72 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER P 63 " --> pdb=" O THR P 74 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.292A pdb=" N LEU P 11 " --> pdb=" O GLU P 105 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS P 50 " --> pdb=" O SER P 53 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.292A pdb=" N LEU P 11 " --> pdb=" O GLU P 105 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU P 90 " --> pdb=" O THR P 97 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR P 97 " --> pdb=" O GLU P 90 " (cutoff:3.500A) 168 hydrogen bonds defined for protein. 372 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: 0.80 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1761 1.35 - 1.47: 1559 1.47 - 1.60: 2287 1.60 - 1.73: 0 1.73 - 1.86: 36 Bond restraints: 5643 Sorted by residual: bond pdb=" N GLY O 100A" pdb=" CA GLY O 100A" ideal model delta sigma weight residual 1.443 1.476 -0.034 1.37e-02 5.33e+03 6.12e+00 bond pdb=" N SER O 100 " pdb=" CA SER O 100 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.17e+00 bond pdb=" C PRO O 100B" pdb=" O PRO O 100B" ideal model delta sigma weight residual 1.235 1.218 0.017 7.90e-03 1.60e+04 4.79e+00 bond pdb=" N PHE O 100C" pdb=" CA PHE O 100C" ideal model delta sigma weight residual 1.458 1.487 -0.029 1.41e-02 5.03e+03 4.28e+00 bond pdb=" N GLN M 39 " pdb=" CA GLN M 39 " ideal model delta sigma weight residual 1.464 1.489 -0.026 1.25e-02 6.40e+03 4.22e+00 ... (remaining 5638 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 7342 2.66 - 5.32: 269 5.32 - 7.98: 40 7.98 - 10.63: 3 10.63 - 13.29: 2 Bond angle restraints: 7656 Sorted by residual: angle pdb=" N GLN P 89 " pdb=" CA GLN P 89 " pdb=" C GLN P 89 " ideal model delta sigma weight residual 108.34 114.78 -6.44 1.64e+00 3.72e-01 1.54e+01 angle pdb=" CA LEU L 78 " pdb=" CB LEU L 78 " pdb=" CG LEU L 78 " ideal model delta sigma weight residual 116.30 129.59 -13.29 3.50e+00 8.16e-02 1.44e+01 angle pdb=" C PHE H 96 " pdb=" CA PHE H 96 " pdb=" CB PHE H 96 " ideal model delta sigma weight residual 109.86 116.58 -6.72 1.80e+00 3.09e-01 1.39e+01 angle pdb=" CB MET P 4 " pdb=" CG MET P 4 " pdb=" SD MET P 4 " ideal model delta sigma weight residual 112.70 101.59 11.11 3.00e+00 1.11e-01 1.37e+01 angle pdb=" C PHE H 52A" pdb=" N ASP H 53 " pdb=" CA ASP H 53 " ideal model delta sigma weight residual 124.31 130.42 -6.11 1.67e+00 3.59e-01 1.34e+01 ... (remaining 7651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 2939 17.13 - 34.27: 245 34.27 - 51.40: 85 51.40 - 68.53: 16 68.53 - 85.66: 10 Dihedral angle restraints: 3295 sinusoidal: 1283 harmonic: 2012 Sorted by residual: dihedral pdb=" CB CYS O 22 " pdb=" SG CYS O 22 " pdb=" SG CYS O 92 " pdb=" CB CYS O 92 " ideal model delta sinusoidal sigma weight residual -86.00 -2.28 -83.72 1 1.00e+01 1.00e-02 8.55e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual -86.00 -4.32 -81.68 1 1.00e+01 1.00e-02 8.21e+01 dihedral pdb=" CB CYS M 22 " pdb=" SG CYS M 22 " pdb=" SG CYS M 92 " pdb=" CB CYS M 92 " ideal model delta sinusoidal sigma weight residual 93.00 35.01 57.99 1 1.00e+01 1.00e-02 4.51e+01 ... (remaining 3292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 495 0.048 - 0.095: 230 0.095 - 0.143: 73 0.143 - 0.190: 11 0.190 - 0.237: 6 Chirality restraints: 815 Sorted by residual: chirality pdb=" CB THR P 102 " pdb=" CA THR P 102 " pdb=" OG1 THR P 102 " pdb=" CG2 THR P 102 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB ILE N 48 " pdb=" CA ILE N 48 " pdb=" CG1 ILE N 48 " pdb=" CG2 ILE N 48 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ASP H 53 " pdb=" N ASP H 53 " pdb=" C ASP H 53 " pdb=" CB ASP H 53 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 812 not shown) Planarity restraints: 983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS L 39 " -0.073 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO L 40 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO L 40 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO L 40 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 36 " 0.030 2.00e-02 2.50e+03 2.17e-02 1.18e+01 pdb=" CG TRP M 36 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP M 36 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP M 36 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP M 36 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP M 36 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP M 36 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 36 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 36 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP M 36 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE L 28 " 0.024 2.00e-02 2.50e+03 1.94e-02 6.57e+00 pdb=" CG PHE L 28 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE L 28 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE L 28 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE L 28 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE L 28 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE L 28 " 0.009 2.00e-02 2.50e+03 ... (remaining 980 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 65 2.60 - 3.17: 4446 3.17 - 3.75: 8175 3.75 - 4.32: 11110 4.32 - 4.90: 18569 Nonbonded interactions: 42365 Sorted by model distance: nonbonded pdb=" OD1 ASP N 82 " pdb=" OH TYR N 86 " model vdw 2.019 3.040 nonbonded pdb=" O ALA P 51 " pdb=" OG SER P 52 " model vdw 2.024 3.040 nonbonded pdb=" OH TYR H 102 " pdb=" OG SER P 67 " model vdw 2.150 3.040 nonbonded pdb=" OE2 GLU N 90 " pdb=" OG1 THR N 92 " model vdw 2.153 3.040 nonbonded pdb=" OD1 ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.160 3.040 ... (remaining 42360 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 'H' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'P' } 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 group one per residue 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: 2.690 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.310 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 5649 Z= 0.224 Angle : 1.151 13.293 7668 Z= 0.645 Chirality : 0.060 0.237 815 Planarity : 0.006 0.110 983 Dihedral : 14.987 85.664 2001 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.78 % Favored : 94.78 % Rotamer: Outliers : 0.67 % Allowed : 23.24 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.31), residues: 690 helix: None (None), residues: 0 sheet: 0.06 (0.31), residues: 225 loop : -0.02 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.002 ARG O 94 TYR 0.027 0.003 TYR P 86 PHE 0.043 0.004 PHE L 28 TRP 0.058 0.003 TRP M 36 HIS 0.011 0.003 HIS M 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.22 ( 5643) covalent geometry : angle 1.13606 / 0.64 ( 7656) SS BOND : bond 0.01042 / 0.55 ( 6) SS BOND : angle 4.77010 / 3.79 ( 12) hydrogen bonds : bond 0.31947 / 20.75 ( 157) hydrogen bonds : angle 10.92852 / 7.61 ( 372) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 217 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 97 TYR cc_start: 0.5988 (m-80) cc_final: 0.5768 (m-10) REVERT: L 82 ASP cc_start: 0.5313 (t0) cc_final: 0.5108 (t0) REVERT: L 90 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7532 (pp20) REVERT: L 91 TYR cc_start: 0.7553 (p90) cc_final: 0.7306 (p90) REVERT: M 19 ARG cc_start: 0.7582 (tpp80) cc_final: 0.6693 (tpp80) REVERT: M 34 MET cc_start: 0.6450 (tpp) cc_final: 0.6199 (mmm) REVERT: M 81 GLU cc_start: 0.5474 (tp30) cc_final: 0.4529 (tp30) REVERT: M 82 MET cc_start: 0.7173 (mmt) cc_final: 0.6875 (mmt) REVERT: M 86 ASP cc_start: 0.7909 (m-30) cc_final: 0.7702 (p0) REVERT: M 94 ARG cc_start: 0.7273 (tmt-80) cc_final: 0.6297 (tpt170) REVERT: N 6 GLN cc_start: 0.5658 (mt0) cc_final: 0.5335 (mm-40) REVERT: O 68 THR cc_start: 0.7327 (m) cc_final: 0.6778 (m) REVERT: O 80 MET cc_start: 0.5717 (tpt) cc_final: 0.4701 (ttt) REVERT: O 105 GLN cc_start: 0.7931 (pm20) cc_final: 0.7186 (pp30) REVERT: P 27 GLN cc_start: 0.7250 (mm-40) cc_final: 0.6688 (tm-30) outliers start: 4 outliers final: 3 residues processed: 219 average time/residue: 0.0903 time to fit residues: 24.6708 Evaluate side-chains 172 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 169 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 27 optimal weight: 0.0970 chunk 64 optimal weight: 0.2980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 93 HIS M 35 HIS ** M 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.167241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.142621 restraints weight = 11437.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.146416 restraints weight = 6901.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.149045 restraints weight = 4864.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.150609 restraints weight = 3804.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.152001 restraints weight = 3215.393| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5649 Z= 0.161 Angle : 0.733 7.449 7668 Z= 0.400 Chirality : 0.049 0.182 815 Planarity : 0.006 0.066 983 Dihedral : 4.912 23.324 772 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.33), residues: 690 helix: None (None), residues: 0 sheet: 0.60 (0.32), residues: 249 loop : -0.04 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 24 TYR 0.015 0.002 TYR N 91 PHE 0.048 0.003 PHE H 52A TRP 0.029 0.002 TRP H 36 HIS 0.006 0.002 HIS O 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 5643) covalent geometry : angle 0.73043 / 0.40 ( 7656) SS BOND : bond 0.00561 / 0.27 ( 6) SS BOND : angle 1.66990 / 1.13 ( 12) hydrogen bonds : bond 0.04526 / 2.93 ( 157) hydrogen bonds : angle 8.09626 / 5.61 ( 372) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.7876 (m100) cc_final: 0.7597 (m100) REVERT: M 82 MET cc_start: 0.6537 (mmt) cc_final: 0.6221 (mmt) REVERT: N 92 THR cc_start: 0.7771 (p) cc_final: 0.7401 (p) REVERT: O 75 LYS cc_start: 0.7895 (mppt) cc_final: 0.7532 (tppt) REVERT: O 80 MET cc_start: 0.6572 (tpt) cc_final: 0.6212 (ttt) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.0809 time to fit residues: 21.3513 Evaluate side-chains 159 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 46 optimal weight: 0.0170 chunk 31 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 overall best weight: 1.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 1 GLN M 31 ASN M 35 HIS ** M 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 27 GLN ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN P 70 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.154961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.126398 restraints weight = 11377.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.130231 restraints weight = 6821.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.132870 restraints weight = 4846.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.134727 restraints weight = 3832.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.135938 restraints weight = 3257.987| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 5649 Z= 0.252 Angle : 0.716 7.081 7668 Z= 0.391 Chirality : 0.048 0.183 815 Planarity : 0.006 0.054 983 Dihedral : 5.289 29.429 772 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.22 % Favored : 94.64 % Rotamer: Outliers : 0.17 % Allowed : 5.02 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.46 (0.32), residues: 258 loop : -0.06 (0.33), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 96 TYR 0.019 0.002 TYR H 91 PHE 0.034 0.003 PHE H 52A TRP 0.016 0.002 TRP H 36 HIS 0.008 0.003 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.25 ( 5643) covalent geometry : angle 0.71094 / 0.39 ( 7656) SS BOND : bond 0.00736 / 0.39 ( 6) SS BOND : angle 2.17605 / 1.54 ( 12) hydrogen bonds : bond 0.04066 / 2.75 ( 157) hydrogen bonds : angle 7.15622 / 4.97 ( 372) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8260 (m100) cc_final: 0.7763 (m100) REVERT: L 26 SER cc_start: 0.9101 (p) cc_final: 0.8755 (t) REVERT: L 82 ASP cc_start: 0.6634 (t0) cc_final: 0.6429 (t0) REVERT: L 83 VAL cc_start: 0.8169 (t) cc_final: 0.7855 (m) REVERT: M 86 ASP cc_start: 0.7802 (m-30) cc_final: 0.7499 (p0) REVERT: N 4 MET cc_start: 0.7652 (ttt) cc_final: 0.7423 (ttt) REVERT: N 14 SER cc_start: 0.7053 (t) cc_final: 0.6697 (p) REVERT: O 20 LEU cc_start: 0.8263 (mt) cc_final: 0.7721 (mp) REVERT: O 29 PHE cc_start: 0.8054 (m-80) cc_final: 0.7669 (m-80) REVERT: O 82 MET cc_start: 0.7419 (ttp) cc_final: 0.6969 (ttp) REVERT: P 27 GLN cc_start: 0.7500 (tm130) cc_final: 0.6799 (tm-30) REVERT: P 86 TYR cc_start: 0.8031 (m-80) cc_final: 0.7751 (m-80) REVERT: P 100 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7431 (pt0) outliers start: 1 outliers final: 1 residues processed: 202 average time/residue: 0.0762 time to fit residues: 20.1250 Evaluate side-chains 155 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 HIS ** M 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 95 ASN P 38 GLN P 70 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.156644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.128100 restraints weight = 11285.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.131966 restraints weight = 6615.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.134775 restraints weight = 4629.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.136450 restraints weight = 3600.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.137858 restraints weight = 3055.209| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 5649 Z= 0.156 Angle : 0.643 7.481 7668 Z= 0.347 Chirality : 0.046 0.185 815 Planarity : 0.005 0.047 983 Dihedral : 5.100 30.268 772 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.51 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.52 (0.32), residues: 258 loop : -0.15 (0.33), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 24 TYR 0.014 0.002 TYR P 86 PHE 0.039 0.002 PHE H 52A TRP 0.015 0.002 TRP M 103 HIS 0.016 0.003 HIS M 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 5643) covalent geometry : angle 0.64030 / 0.35 ( 7656) SS BOND : bond 0.00494 / 0.27 ( 6) SS BOND : angle 1.49398 / 0.98 ( 12) hydrogen bonds : bond 0.03449 / 2.35 ( 157) hydrogen bonds : angle 6.62555 / 4.60 ( 372) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8395 (m100) cc_final: 0.8087 (m100) REVERT: H 82 ASP cc_start: 0.8794 (p0) cc_final: 0.8277 (p0) REVERT: L 26 SER cc_start: 0.9135 (p) cc_final: 0.8837 (t) REVERT: L 83 VAL cc_start: 0.7923 (t) cc_final: 0.7556 (m) REVERT: M 34 MET cc_start: 0.7872 (mmm) cc_final: 0.7579 (mpp) REVERT: M 86 ASP cc_start: 0.7863 (m-30) cc_final: 0.7536 (p0) REVERT: N 14 SER cc_start: 0.7018 (t) cc_final: 0.6661 (p) REVERT: O 16 ARG cc_start: 0.7799 (mtm-85) cc_final: 0.7306 (mtm-85) REVERT: O 20 LEU cc_start: 0.8179 (mt) cc_final: 0.7755 (mp) REVERT: O 46 GLU cc_start: 0.8553 (tp30) cc_final: 0.8092 (tm-30) REVERT: O 75 LYS cc_start: 0.8405 (mppt) cc_final: 0.7920 (tppt) REVERT: O 82 MET cc_start: 0.7508 (ttp) cc_final: 0.6466 (ttm) REVERT: P 4 MET cc_start: 0.7266 (mmm) cc_final: 0.6847 (mmm) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.0767 time to fit residues: 19.9829 Evaluate side-chains 160 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 30 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 HIS M 93 HIS P 27 GLN P 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.153279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.124092 restraints weight = 11568.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.127848 restraints weight = 7000.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.130433 restraints weight = 4999.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.131970 restraints weight = 3978.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.133241 restraints weight = 3434.918| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5649 Z= 0.185 Angle : 0.632 7.136 7668 Z= 0.343 Chirality : 0.047 0.187 815 Planarity : 0.005 0.043 983 Dihedral : 5.088 30.442 772 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.80 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.47 (0.32), residues: 258 loop : -0.26 (0.33), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 19 TYR 0.014 0.002 TYR L 36 PHE 0.030 0.003 PHE H 52A TRP 0.014 0.002 TRP M 103 HIS 0.017 0.004 HIS M 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 ( 5643) covalent geometry : angle 0.63023 / 0.34 ( 7656) SS BOND : bond 0.00483 / 0.27 ( 6) SS BOND : angle 1.44105 / 0.95 ( 12) hydrogen bonds : bond 0.03661 / 2.48 ( 157) hydrogen bonds : angle 6.34231 / 4.39 ( 372) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8400 (m100) cc_final: 0.7949 (m100) REVERT: H 82 ASP cc_start: 0.8752 (p0) cc_final: 0.8251 (p0) REVERT: L 26 SER cc_start: 0.9129 (p) cc_final: 0.8880 (t) REVERT: L 68 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7038 (mm-30) REVERT: L 83 VAL cc_start: 0.8139 (t) cc_final: 0.7770 (m) REVERT: M 34 MET cc_start: 0.8148 (mmm) cc_final: 0.7462 (mpp) REVERT: M 86 ASP cc_start: 0.7843 (m-30) cc_final: 0.7602 (p0) REVERT: N 14 SER cc_start: 0.7338 (t) cc_final: 0.6902 (p) REVERT: N 100 GLN cc_start: 0.8046 (mm110) cc_final: 0.7825 (mm110) REVERT: O 75 LYS cc_start: 0.8465 (mppt) cc_final: 0.7948 (tppt) REVERT: O 82 MET cc_start: 0.7512 (ttp) cc_final: 0.6851 (ttm) REVERT: P 4 MET cc_start: 0.7238 (mmm) cc_final: 0.7012 (mmm) REVERT: P 27 GLN cc_start: 0.7261 (tm130) cc_final: 0.6718 (tm-30) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.0751 time to fit residues: 18.6804 Evaluate side-chains 164 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 24 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 6 optimal weight: 0.0370 chunk 49 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN M 35 HIS ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN ** P 89 GLN ** 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 = 0.4073 r_free = 0.4073 target = 0.155434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.126795 restraints weight = 11344.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.130557 restraints weight = 6769.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.133301 restraints weight = 4824.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.135155 restraints weight = 3797.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.136236 restraints weight = 3216.623| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5649 Z= 0.135 Angle : 0.619 7.414 7668 Z= 0.332 Chirality : 0.047 0.189 815 Planarity : 0.005 0.048 983 Dihedral : 5.066 29.789 772 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.51 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.41 (0.32), residues: 258 loop : -0.34 (0.33), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 38 TYR 0.013 0.002 TYR H 91 PHE 0.041 0.003 PHE H 52A TRP 0.015 0.002 TRP H 103 HIS 0.014 0.002 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 5643) covalent geometry : angle 0.61706 / 0.33 ( 7656) SS BOND : bond 0.00527 / 0.30 ( 6) SS BOND : angle 1.38187 / 0.87 ( 12) hydrogen bonds : bond 0.03235 / 2.13 ( 157) hydrogen bonds : angle 6.03982 / 4.21 ( 372) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 115 ASN cc_start: 0.7434 (t0) cc_final: 0.7233 (t0) REVERT: H 36 TRP cc_start: 0.8387 (m100) cc_final: 0.7888 (m100) REVERT: H 82 ASP cc_start: 0.8711 (p0) cc_final: 0.8181 (p0) REVERT: L 68 GLU cc_start: 0.7754 (mm-30) cc_final: 0.6971 (mm-30) REVERT: L 83 VAL cc_start: 0.8039 (t) cc_final: 0.7677 (m) REVERT: M 34 MET cc_start: 0.8029 (mmm) cc_final: 0.7451 (mpp) REVERT: N 4 MET cc_start: 0.7710 (ttt) cc_final: 0.7364 (ttt) REVERT: N 14 SER cc_start: 0.7344 (t) cc_final: 0.6884 (p) REVERT: N 90 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7521 (tp30) REVERT: N 100 GLN cc_start: 0.7986 (mm110) cc_final: 0.7740 (mm110) REVERT: O 59 TYR cc_start: 0.7308 (m-80) cc_final: 0.7038 (m-10) REVERT: O 75 LYS cc_start: 0.8467 (mppt) cc_final: 0.7958 (tppt) REVERT: O 82 MET cc_start: 0.7521 (ttp) cc_final: 0.6884 (ttm) REVERT: O 105 GLN cc_start: 0.7844 (tp-100) cc_final: 0.7571 (tp-100) REVERT: P 4 MET cc_start: 0.7166 (mmm) cc_final: 0.6866 (mmm) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.0678 time to fit residues: 17.5304 Evaluate side-chains 159 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 30 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 HIS ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN ** P 89 GLN ** 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 = 0.4084 r_free = 0.4084 target = 0.155759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.127155 restraints weight = 11275.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.131011 restraints weight = 6623.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.133668 restraints weight = 4664.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.135473 restraints weight = 3674.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.136557 restraints weight = 3118.518| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5649 Z= 0.137 Angle : 0.620 7.256 7668 Z= 0.332 Chirality : 0.047 0.201 815 Planarity : 0.005 0.042 983 Dihedral : 4.976 30.336 772 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.67 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.41 (0.32), residues: 258 loop : -0.40 (0.33), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 24 TYR 0.013 0.002 TYR P 86 PHE 0.032 0.002 PHE H 52A TRP 0.015 0.002 TRP H 103 HIS 0.012 0.002 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 5643) covalent geometry : angle 0.61846 / 0.33 ( 7656) SS BOND : bond 0.00488 / 0.26 ( 6) SS BOND : angle 1.38204 / 0.88 ( 12) hydrogen bonds : bond 0.03217 / 2.13 ( 157) hydrogen bonds : angle 5.89266 / 4.09 ( 372) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8384 (m100) cc_final: 0.7971 (m100) REVERT: H 82 ASP cc_start: 0.8726 (p0) cc_final: 0.8375 (p0) REVERT: L 68 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7038 (mm-30) REVERT: L 83 VAL cc_start: 0.8082 (t) cc_final: 0.7709 (m) REVERT: M 34 MET cc_start: 0.8056 (mmm) cc_final: 0.7411 (mpp) REVERT: M 86 ASP cc_start: 0.7863 (m-30) cc_final: 0.7537 (m-30) REVERT: N 4 MET cc_start: 0.7601 (ttt) cc_final: 0.7212 (ttt) REVERT: N 14 SER cc_start: 0.7369 (t) cc_final: 0.6893 (p) REVERT: O 34 MET cc_start: 0.7170 (ptm) cc_final: 0.6963 (ptt) REVERT: O 46 GLU cc_start: 0.8487 (tp30) cc_final: 0.7985 (tm-30) REVERT: O 59 TYR cc_start: 0.7172 (m-80) cc_final: 0.6862 (m-10) REVERT: O 75 LYS cc_start: 0.8698 (mppt) cc_final: 0.7958 (tppt) REVERT: O 82 MET cc_start: 0.7510 (ttp) cc_final: 0.6952 (ttm) REVERT: O 105 GLN cc_start: 0.7841 (tp-100) cc_final: 0.7608 (tp-100) REVERT: P 86 TYR cc_start: 0.7804 (m-80) cc_final: 0.7522 (m-80) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.0727 time to fit residues: 17.7518 Evaluate side-chains 158 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 40 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 117 ASN M 35 HIS ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 27 GLN P 38 GLN ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.152455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.123134 restraints weight = 11447.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.126825 restraints weight = 6893.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.129370 restraints weight = 4950.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.131114 restraints weight = 3944.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.131891 restraints weight = 3378.826| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 5649 Z= 0.176 Angle : 0.646 7.453 7668 Z= 0.350 Chirality : 0.047 0.185 815 Planarity : 0.005 0.042 983 Dihedral : 5.080 30.495 772 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.81 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.34 (0.32), residues: 258 loop : -0.53 (0.33), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 94 TYR 0.018 0.002 TYR P 86 PHE 0.042 0.003 PHE H 52A TRP 0.024 0.002 TRP H 103 HIS 0.008 0.002 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 ( 5643) covalent geometry : angle 0.64249 / 0.35 ( 7656) SS BOND : bond 0.00609 / 0.32 ( 6) SS BOND : angle 1.74755 / 1.20 ( 12) hydrogen bonds : bond 0.03316 / 2.19 ( 157) hydrogen bonds : angle 5.94565 / 4.12 ( 372) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 115 ASN cc_start: 0.7719 (t0) cc_final: 0.7409 (t0) REVERT: H 36 TRP cc_start: 0.8525 (m100) cc_final: 0.8065 (m100) REVERT: H 82 ASP cc_start: 0.8770 (p0) cc_final: 0.8424 (p0) REVERT: L 83 VAL cc_start: 0.8228 (t) cc_final: 0.7805 (m) REVERT: L 91 TYR cc_start: 0.8438 (p90) cc_final: 0.8153 (p90) REVERT: M 46 GLU cc_start: 0.8252 (pt0) cc_final: 0.7743 (mp0) REVERT: M 98 ASP cc_start: 0.8360 (t0) cc_final: 0.7964 (t0) REVERT: N 4 MET cc_start: 0.7659 (ttt) cc_final: 0.7294 (ttt) REVERT: N 14 SER cc_start: 0.7516 (t) cc_final: 0.7022 (p) REVERT: N 100 GLN cc_start: 0.8092 (mm110) cc_final: 0.7727 (mm110) REVERT: O 34 MET cc_start: 0.7195 (ptm) cc_final: 0.6764 (ptm) REVERT: O 46 GLU cc_start: 0.8543 (tp30) cc_final: 0.8194 (tm-30) REVERT: O 59 TYR cc_start: 0.7275 (m-80) cc_final: 0.6910 (m-10) REVERT: O 75 LYS cc_start: 0.8808 (mppt) cc_final: 0.8037 (tppt) REVERT: O 82 MET cc_start: 0.7633 (ttp) cc_final: 0.7079 (ttm) REVERT: O 105 GLN cc_start: 0.7862 (tp-100) cc_final: 0.7634 (tp-100) REVERT: P 27 GLN cc_start: 0.7286 (tm130) cc_final: 0.6573 (tm-30) REVERT: P 105 GLU cc_start: 0.8076 (pp20) cc_final: 0.7805 (pp20) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.0786 time to fit residues: 20.4241 Evaluate side-chains 164 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 60 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 93 HIS ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 HIS ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN ** P 89 GLN ** 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 = 0.4066 r_free = 0.4066 target = 0.154177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.125389 restraints weight = 11358.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.129266 restraints weight = 6653.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.131749 restraints weight = 4666.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.133531 restraints weight = 3710.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.134556 restraints weight = 3150.116| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.5738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5649 Z= 0.148 Angle : 0.663 7.507 7668 Z= 0.353 Chirality : 0.047 0.198 815 Planarity : 0.005 0.052 983 Dihedral : 5.030 30.457 772 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.81 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.56 (0.33), residues: 255 loop : -0.63 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 24 TYR 0.016 0.002 TYR H 32 PHE 0.034 0.002 PHE H 52A TRP 0.017 0.002 TRP M 36 HIS 0.005 0.002 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 5643) covalent geometry : angle 0.65604 / 0.35 ( 7656) SS BOND : bond 0.00675 / 0.37 ( 6) SS BOND : angle 2.58474 / 1.54 ( 12) hydrogen bonds : bond 0.03285 / 2.15 ( 157) hydrogen bonds : angle 5.97826 / 4.18 ( 372) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 115 ASN cc_start: 0.7617 (t0) cc_final: 0.7345 (t0) REVERT: H 36 TRP cc_start: 0.8435 (m100) cc_final: 0.8043 (m100) REVERT: H 82 ASP cc_start: 0.8665 (p0) cc_final: 0.8319 (p0) REVERT: L 83 VAL cc_start: 0.8146 (t) cc_final: 0.7717 (m) REVERT: L 91 TYR cc_start: 0.8455 (p90) cc_final: 0.8145 (p90) REVERT: M 46 GLU cc_start: 0.8257 (pt0) cc_final: 0.7734 (mp0) REVERT: N 4 MET cc_start: 0.7706 (ttt) cc_final: 0.7354 (ttt) REVERT: N 14 SER cc_start: 0.7529 (t) cc_final: 0.7025 (p) REVERT: N 100 GLN cc_start: 0.8018 (mm110) cc_final: 0.7702 (mm110) REVERT: O 46 GLU cc_start: 0.8517 (tp30) cc_final: 0.8229 (tm-30) REVERT: O 59 TYR cc_start: 0.7189 (m-80) cc_final: 0.6830 (m-10) REVERT: O 68 THR cc_start: 0.6962 (m) cc_final: 0.6739 (p) REVERT: O 75 LYS cc_start: 0.8549 (mppt) cc_final: 0.8067 (tppt) REVERT: O 82 MET cc_start: 0.7551 (ttp) cc_final: 0.6999 (ttm) REVERT: P 86 TYR cc_start: 0.7616 (m-80) cc_final: 0.7339 (m-80) REVERT: P 105 GLU cc_start: 0.8025 (pp20) cc_final: 0.7769 (pp20) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.0674 time to fit residues: 17.5353 Evaluate side-chains 165 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 47 optimal weight: 0.0970 chunk 53 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 HIS ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN ** P 89 GLN ** 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 = 0.4054 r_free = 0.4054 target = 0.153885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.124880 restraints weight = 11461.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.128575 restraints weight = 6936.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.131033 restraints weight = 4964.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.132726 restraints weight = 3977.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.133810 restraints weight = 3420.659| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.5922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 5649 Z= 0.164 Angle : 0.666 8.439 7668 Z= 0.355 Chirality : 0.047 0.239 815 Planarity : 0.005 0.042 983 Dihedral : 5.035 30.665 772 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.09 % Favored : 93.77 % Rotamer: Outliers : 0.17 % Allowed : 0.67 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.53 (0.33), residues: 255 loop : -0.69 (0.33), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 24 TYR 0.019 0.002 TYR P 86 PHE 0.027 0.003 PHE H 52A TRP 0.053 0.002 TRP H 103 HIS 0.014 0.002 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 5643) covalent geometry : angle 0.65943 / 0.35 ( 7656) SS BOND : bond 0.00489 / 0.26 ( 6) SS BOND : angle 2.44662 / 1.50 ( 12) hydrogen bonds : bond 0.03281 / 2.16 ( 157) hydrogen bonds : angle 5.98582 / 4.19 ( 372) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 115 ASN cc_start: 0.7714 (t0) cc_final: 0.7502 (t0) REVERT: H 36 TRP cc_start: 0.8411 (m100) cc_final: 0.8020 (m100) REVERT: H 82 ASP cc_start: 0.8584 (p0) cc_final: 0.8213 (p0) REVERT: L 83 VAL cc_start: 0.8262 (t) cc_final: 0.7833 (m) REVERT: L 91 TYR cc_start: 0.8511 (p90) cc_final: 0.8205 (p90) REVERT: N 4 MET cc_start: 0.7748 (ttt) cc_final: 0.7489 (ttt) REVERT: N 14 SER cc_start: 0.7508 (t) cc_final: 0.7003 (p) REVERT: N 100 GLN cc_start: 0.8033 (mm110) cc_final: 0.7787 (tp40) REVERT: O 46 GLU cc_start: 0.8514 (tp30) cc_final: 0.8269 (tm-30) REVERT: O 59 TYR cc_start: 0.7196 (m-80) cc_final: 0.6830 (m-10) REVERT: O 68 THR cc_start: 0.6961 (m) cc_final: 0.6707 (p) REVERT: O 75 LYS cc_start: 0.8740 (mppt) cc_final: 0.8025 (tppt) REVERT: O 82 MET cc_start: 0.7443 (ttp) cc_final: 0.6965 (ttm) REVERT: P 105 GLU cc_start: 0.8025 (pp20) cc_final: 0.7707 (pp20) outliers start: 1 outliers final: 0 residues processed: 192 average time/residue: 0.0657 time to fit residues: 16.9708 Evaluate side-chains 160 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 9 optimal weight: 0.0670 chunk 41 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 54 optimal weight: 0.0030 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 HIS ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN ** P 89 GLN ** 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 = 0.4071 r_free = 0.4071 target = 0.155358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.126128 restraints weight = 11354.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.129822 restraints weight = 6922.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.132332 restraints weight = 4994.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.133961 restraints weight = 4004.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.134730 restraints weight = 3452.095| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5649 Z= 0.144 Angle : 0.656 8.338 7668 Z= 0.349 Chirality : 0.047 0.249 815 Planarity : 0.005 0.043 983 Dihedral : 4.980 30.983 772 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.81 % Favored : 93.04 % Rotamer: Outliers : 0.17 % Allowed : 0.17 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.55 (0.33), residues: 255 loop : -0.72 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 24 TYR 0.015 0.002 TYR P 86 PHE 0.023 0.002 PHE H 52A TRP 0.018 0.002 TRP M 36 HIS 0.008 0.002 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 5643) covalent geometry : angle 0.64966 / 0.35 ( 7656) SS BOND : bond 0.00521 / 0.27 ( 6) SS BOND : angle 2.43667 / 1.47 ( 12) hydrogen bonds : bond 0.03140 / 2.05 ( 157) hydrogen bonds : angle 5.92007 / 4.15 ( 372) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1219.15 seconds wall clock time: 21 minutes 49.55 seconds (1309.55 seconds total)