Starting phenix.real_space_refine on Tue Feb 3 21:50:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t3p_55504/02_2026/9t3p_55504.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t3p_55504/02_2026/9t3p_55504.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9t3p_55504/02_2026/9t3p_55504.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t3p_55504/02_2026/9t3p_55504.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9t3p_55504/02_2026/9t3p_55504.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t3p_55504/02_2026/9t3p_55504.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.033 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 27 5.16 5 C 4653 2.51 5 N 1197 2.21 5 O 1530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7407 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain breaks: 1 Chain: "B" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain breaks: 1 Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain breaks: 1 Chain: "D" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain breaks: 1 Chain: "E" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain breaks: 1 Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain breaks: 1 Chain: "G" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain breaks: 1 Chain: "H" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain breaks: 1 Chain: "I" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain breaks: 1 Time building chain proxies: 1.79, per 1000 atoms: 0.24 Number of scatterers: 7407 At special positions: 0 Unit cell: (102.86, 104.25, 65.33, 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 27 16.00 O 1530 8.00 N 1197 7.00 C 4653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS B 123 " distance=1.64 Simple disulfide: pdb=" SG CYS A 123 " - pdb=" SG CYS I 117 " distance=1.51 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS C 123 " distance=1.94 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS D 123 " distance=2.01 Simple disulfide: pdb=" SG CYS D 117 " - pdb=" SG CYS E 123 " distance=1.82 Simple disulfide: pdb=" SG CYS E 117 " - pdb=" SG CYS F 123 " distance=1.77 Simple disulfide: pdb=" SG CYS F 117 " - pdb=" SG CYS G 123 " distance=1.89 Simple disulfide: pdb=" SG CYS G 117 " - pdb=" SG CYS H 123 " distance=1.46 Simple disulfide: pdb=" SG CYS H 117 " - pdb=" SG CYS I 123 " distance=2.16 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: 0.69 Conformation dependent library (CDL) restraints added in 290.7 milliseconds 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1818 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 54.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 17 removed outlier: 6.414A pdb=" N THR A 82 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LYS B 40 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER A 84 " --> pdb=" O LYS B 40 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR B 34 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP B 97 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL B 93 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER B 64 " --> pdb=" O ILE B 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 77 removed outlier: 4.383A pdb=" N SER A 64 " --> pdb=" O ILE A 96 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL A 93 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP A 97 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR A 34 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 15.696A pdb=" N THR I 82 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 10.867A pdb=" N VAL A 36 " --> pdb=" O THR I 82 " (cutoff:3.500A) removed outlier: 10.047A pdb=" N SER I 84 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE A 38 " --> pdb=" O SER I 84 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N THR I 86 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LYS A 40 " --> pdb=" O THR I 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 17 removed outlier: 10.763A pdb=" N THR B 82 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE C 38 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS C 40 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR C 34 " --> pdb=" O ASP C 97 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP C 97 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL C 93 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER C 64 " --> pdb=" O ILE C 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 5 through 17 removed outlier: 10.724A pdb=" N THR C 82 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE D 38 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS D 40 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N THR D 34 " --> pdb=" O ASP D 97 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP D 97 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL D 93 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER D 64 " --> pdb=" O ILE D 96 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 5 through 17 removed outlier: 10.538A pdb=" N THR D 82 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE E 38 " --> pdb=" O THR D 82 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS E 40 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N THR E 34 " --> pdb=" O ASP E 97 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP E 97 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL E 93 " --> pdb=" O ILE E 38 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER E 64 " --> pdb=" O ILE E 96 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 5 through 17 removed outlier: 10.322A pdb=" N THR E 82 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE F 38 " --> pdb=" O THR E 82 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS F 40 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N THR F 34 " --> pdb=" O ASP F 97 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP F 97 " --> pdb=" O THR F 34 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL F 93 " --> pdb=" O ILE F 38 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER F 64 " --> pdb=" O ILE F 96 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 5 through 17 removed outlier: 10.375A pdb=" N THR F 82 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE G 38 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS G 40 " --> pdb=" O SER F 84 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N THR G 34 " --> pdb=" O ASP G 97 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP G 97 " --> pdb=" O THR G 34 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL G 93 " --> pdb=" O ILE G 38 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER G 64 " --> pdb=" O ILE G 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 5 through 17 removed outlier: 10.130A pdb=" N THR G 82 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ILE H 38 " --> pdb=" O THR G 82 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS H 40 " --> pdb=" O SER G 84 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N THR H 34 " --> pdb=" O ASP H 97 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP H 97 " --> pdb=" O THR H 34 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL H 93 " --> pdb=" O ILE H 38 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER H 64 " --> pdb=" O ILE H 96 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 5 through 17 removed outlier: 10.235A pdb=" N THR H 82 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE I 38 " --> pdb=" O THR H 82 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS I 40 " --> pdb=" O SER H 84 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR I 34 " --> pdb=" O ASP I 97 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP I 97 " --> pdb=" O THR I 34 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL I 93 " --> pdb=" O ILE I 38 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER I 64 " --> pdb=" O ILE I 96 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1041 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1844 1.33 - 1.45: 1426 1.45 - 1.57: 4218 1.57 - 1.69: 0 1.69 - 1.81: 27 Bond restraints: 7515 Sorted by residual: bond pdb=" CZ ARG B 121 " pdb=" NH2 ARG B 121 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.06e+01 bond pdb=" CZ ARG D 121 " pdb=" NH2 ARG D 121 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.01e+01 bond pdb=" CZ ARG G 109 " pdb=" NH2 ARG G 109 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.62e+00 bond pdb=" CZ ARG E 121 " pdb=" NH2 ARG E 121 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.31e+00 bond pdb=" CZ ARG H 57 " pdb=" NH2 ARG H 57 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.29e+00 ... (remaining 7510 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 7001 1.25 - 2.49: 2414 2.49 - 3.74: 714 3.74 - 4.99: 99 4.99 - 6.23: 14 Bond angle restraints: 10242 Sorted by residual: angle pdb=" OE1 GLN I 113 " pdb=" CD GLN I 113 " pdb=" NE2 GLN I 113 " ideal model delta sigma weight residual 122.60 119.24 3.36 1.00e+00 1.00e+00 1.13e+01 angle pdb=" OE1 GLN I 91 " pdb=" CD GLN I 91 " pdb=" NE2 GLN I 91 " ideal model delta sigma weight residual 122.60 119.25 3.35 1.00e+00 1.00e+00 1.12e+01 angle pdb=" OD1 ASN A 56 " pdb=" CG ASN A 56 " pdb=" ND2 ASN A 56 " ideal model delta sigma weight residual 122.60 119.31 3.29 1.00e+00 1.00e+00 1.09e+01 angle pdb=" CA PHE A 112 " pdb=" CB PHE A 112 " pdb=" CG PHE A 112 " ideal model delta sigma weight residual 113.80 117.06 -3.26 1.00e+00 1.00e+00 1.06e+01 angle pdb=" OE1 GLN E 91 " pdb=" CD GLN E 91 " pdb=" NE2 GLN E 91 " ideal model delta sigma weight residual 122.60 119.40 3.20 1.00e+00 1.00e+00 1.02e+01 ... (remaining 10237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.76: 4291 15.76 - 31.52: 181 31.52 - 47.28: 19 47.28 - 63.04: 0 63.04 - 78.80: 9 Dihedral angle restraints: 4500 sinusoidal: 1692 harmonic: 2808 Sorted by residual: dihedral pdb=" CA SER G 94 " pdb=" C SER G 94 " pdb=" N VAL G 95 " pdb=" CA VAL G 95 " ideal model delta harmonic sigma weight residual 180.00 161.53 18.47 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA SER B 94 " pdb=" C SER B 94 " pdb=" N VAL B 95 " pdb=" CA VAL B 95 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA SER A 94 " pdb=" C SER A 94 " pdb=" N VAL A 95 " pdb=" CA VAL A 95 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 4497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 561 0.047 - 0.094: 401 0.094 - 0.140: 193 0.140 - 0.187: 78 0.187 - 0.234: 27 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CA ASP I 89 " pdb=" N ASP I 89 " pdb=" C ASP I 89 " pdb=" CB ASP I 89 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ASP B 89 " pdb=" N ASP B 89 " pdb=" C ASP B 89 " pdb=" CB ASP B 89 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA ASP E 89 " pdb=" N ASP E 89 " pdb=" C ASP E 89 " pdb=" CB ASP E 89 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1257 not shown) Planarity restraints: 1296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 110 " 0.059 2.00e-02 2.50e+03 3.18e-02 2.02e+01 pdb=" CG TYR C 110 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR C 110 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR C 110 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR C 110 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR C 110 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR C 110 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 110 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 110 " 0.060 2.00e-02 2.50e+03 3.17e-02 2.01e+01 pdb=" CG TYR D 110 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR D 110 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR D 110 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR D 110 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR D 110 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR D 110 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 110 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 110 " -0.057 2.00e-02 2.50e+03 3.09e-02 1.91e+01 pdb=" CG TYR E 110 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR E 110 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR E 110 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR E 110 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR E 110 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR E 110 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 110 " -0.047 2.00e-02 2.50e+03 ... (remaining 1293 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 23 2.62 - 3.19: 5932 3.19 - 3.76: 10772 3.76 - 4.33: 16241 4.33 - 4.90: 28304 Nonbonded interactions: 61272 Sorted by model distance: nonbonded pdb=" OG SER A 48 " pdb=" NZ LYS B 118 " model vdw 2.048 3.120 nonbonded pdb=" CA LYS A 118 " pdb=" O LEU B 124 " model vdw 2.209 3.470 nonbonded pdb=" N LYS A 118 " pdb=" SG CYS B 123 " model vdw 2.401 3.480 nonbonded pdb=" N SER F 119 " pdb=" O LEU G 124 " model vdw 2.433 3.120 nonbonded pdb=" OG SER G 48 " pdb=" NZ LYS H 118 " model vdw 2.441 3.120 ... (remaining 61267 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 0.060 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.530 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2517 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 : 0.016 0.573 7524 Z= 0.855 Angle : 1.395 25.580 10260 Z= 0.876 Chirality : 0.080 0.234 1260 Planarity : 0.006 0.032 1296 Dihedral : 9.859 78.799 2655 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.46 % Allowed : 0.57 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.72 (0.28), residues: 927 helix: None (None), residues: 0 sheet: 2.32 (0.21), residues: 549 loop : 1.06 (0.35), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 109 TYR 0.060 0.012 TYR D 110 PHE 0.027 0.007 PHE E 112 TRP 0.040 0.013 TRP B 39 Details of bonding type rmsd covalent geometry : bond 0.01197 ( 7515) covalent geometry : angle 1.35859 (10242) SS BOND : bond 0.31895 ( 9) SS BOND : angle 7.68336 ( 18) hydrogen bonds : bond 0.12973 ( 392) hydrogen bonds : angle 7.23872 ( 1041) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 187 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 ASN cc_start: 0.4615 (t0) cc_final: 0.4138 (t160) REVERT: C 123 CYS cc_start: 0.3471 (OUTLIER) cc_final: 0.2745 (t) REVERT: H 123 CYS cc_start: 0.2575 (OUTLIER) cc_final: 0.0292 (p) REVERT: I 112 PHE cc_start: -0.0554 (m-80) cc_final: -0.1367 (m-80) outliers start: 4 outliers final: 4 residues processed: 191 average time/residue: 0.4303 time to fit residues: 88.1689 Evaluate side-chains 76 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain H residue 123 CYS Chi-restraints excluded: chain I residue 105 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 ASN B 73 ASN C 113 GLN D 9 ASN E 9 ASN F 37 ASN F 66 GLN I 73 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5304 r_free = 0.5304 target = 0.155711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.5137 r_free = 0.5137 target = 0.140759 restraints weight = 35839.779| |-----------------------------------------------------------------------------| r_work (start): 0.5118 rms_B_bonded: 8.13 r_work (final): 0.5118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4811 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7524 Z= 0.195 Angle : 0.804 11.318 10260 Z= 0.433 Chirality : 0.053 0.177 1260 Planarity : 0.006 0.070 1296 Dihedral : 6.630 53.251 1035 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.09 % Allowed : 10.31 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.29), residues: 927 helix: None (None), residues: 0 sheet: 1.81 (0.22), residues: 549 loop : 0.47 (0.35), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 109 TYR 0.018 0.003 TYR I 85 PHE 0.032 0.004 PHE A 11 TRP 0.025 0.005 TRP D 39 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 7515) covalent geometry : angle 0.80418 (10242) SS BOND : bond 0.01570 ( 9) SS BOND : angle 0.86829 ( 18) hydrogen bonds : bond 0.04757 ( 392) hydrogen bonds : angle 6.33170 ( 1041) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 TYR cc_start: 0.6559 (t80) cc_final: 0.6226 (OUTLIER) REVERT: C 40 LYS cc_start: 0.8647 (pttt) cc_final: 0.8352 (pmmt) REVERT: C 88 PHE cc_start: 0.7669 (m-80) cc_final: 0.7442 (m-80) REVERT: C 112 PHE cc_start: 0.7913 (m-80) cc_final: 0.6820 (m-10) REVERT: C 113 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7408 (mt0) REVERT: D 10 GLU cc_start: 0.8771 (pm20) cc_final: 0.8396 (mp0) REVERT: D 40 LYS cc_start: 0.7784 (pptt) cc_final: 0.7477 (tmmt) REVERT: E 66 GLN cc_start: 0.7240 (pp30) cc_final: 0.6898 (pm20) REVERT: G 105 TYR cc_start: 0.7487 (t80) cc_final: 0.7182 (t80) REVERT: H 105 TYR cc_start: 0.7598 (t80) cc_final: 0.7389 (t80) REVERT: I 105 TYR cc_start: 0.7025 (t80) cc_final: 0.6532 (t80) outliers start: 27 outliers final: 13 residues processed: 104 average time/residue: 0.4161 time to fit residues: 46.4711 Evaluate side-chains 75 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain I residue 95 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 78 optimal weight: 7.9990 chunk 54 optimal weight: 20.0000 chunk 28 optimal weight: 0.6980 chunk 87 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 68 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN F 73 ASN G 73 ASN H 73 ASN I 66 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5235 r_free = 0.5235 target = 0.144605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5058 r_free = 0.5058 target = 0.127155 restraints weight = 27846.637| |-----------------------------------------------------------------------------| r_work (start): 0.5024 rms_B_bonded: 7.75 r_work (final): 0.5024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5552 moved from start: 0.7777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 7524 Z= 0.215 Angle : 0.802 10.721 10260 Z= 0.437 Chirality : 0.054 0.323 1260 Planarity : 0.005 0.079 1296 Dihedral : 6.475 43.241 1028 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 22.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.63 % Allowed : 12.03 % Favored : 85.34 % 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: 0.51 (0.28), residues: 927 helix: None (None), residues: 0 sheet: 0.74 (0.22), residues: 504 loop : -0.05 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 109 TYR 0.029 0.003 TYR A 110 PHE 0.028 0.004 PHE I 11 TRP 0.021 0.004 TRP B 39 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 7515) covalent geometry : angle 0.80216 (10242) SS BOND : bond 0.00298 ( 9) SS BOND : angle 0.60411 ( 18) hydrogen bonds : bond 0.04747 ( 392) hydrogen bonds : angle 7.58259 ( 1041) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 TYR cc_start: 0.7228 (t80) cc_final: 0.6735 (t80) REVERT: B 105 TYR cc_start: 0.6178 (t80) cc_final: 0.5860 (OUTLIER) REVERT: C 40 LYS cc_start: 0.8828 (pttt) cc_final: 0.8569 (pmmt) REVERT: C 88 PHE cc_start: 0.8437 (m-80) cc_final: 0.7877 (m-80) REVERT: D 10 GLU cc_start: 0.8829 (pm20) cc_final: 0.8612 (mp0) REVERT: D 11 PHE cc_start: 0.8056 (p90) cc_final: 0.7842 (p90) REVERT: D 121 ARG cc_start: 0.7756 (mtt180) cc_final: 0.7504 (mmp-170) REVERT: F 109 ARG cc_start: 0.2959 (OUTLIER) cc_final: 0.2407 (ppt170) REVERT: G 105 TYR cc_start: 0.7431 (t80) cc_final: 0.7216 (t80) REVERT: H 105 TYR cc_start: 0.7692 (t80) cc_final: 0.7317 (t80) REVERT: I 89 ASP cc_start: 0.7356 (p0) cc_final: 0.7141 (p0) REVERT: I 105 TYR cc_start: 0.7198 (t80) cc_final: 0.6516 (t80) REVERT: I 112 PHE cc_start: 0.0466 (m-80) cc_final: 0.0247 (m-80) outliers start: 23 outliers final: 19 residues processed: 103 average time/residue: 0.3407 time to fit residues: 38.0684 Evaluate side-chains 80 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain C residue 9 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 123 CYS Chi-restraints excluded: chain I residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 52 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5183 r_free = 0.5183 target = 0.137137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4974 r_free = 0.4974 target = 0.116824 restraints weight = 30761.706| |-----------------------------------------------------------------------------| r_work (start): 0.4982 rms_B_bonded: 9.91 r_work (final): 0.4982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6066 moved from start: 0.9213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7524 Z= 0.190 Angle : 0.737 10.676 10260 Z= 0.398 Chirality : 0.052 0.172 1260 Planarity : 0.005 0.057 1296 Dihedral : 6.230 36.384 1026 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 22.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.55 % Allowed : 14.09 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.28), residues: 927 helix: None (None), residues: 0 sheet: 0.21 (0.23), residues: 495 loop : -0.31 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 109 TYR 0.058 0.003 TYR F 105 PHE 0.024 0.003 PHE G 112 TRP 0.020 0.003 TRP B 39 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 7515) covalent geometry : angle 0.73738 (10242) SS BOND : bond 0.00115 ( 9) SS BOND : angle 0.71013 ( 18) hydrogen bonds : bond 0.04277 ( 392) hydrogen bonds : angle 7.57569 ( 1041) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 TYR cc_start: 0.8214 (p90) cc_final: 0.7991 (p90) REVERT: C 88 PHE cc_start: 0.9056 (m-80) cc_final: 0.8193 (m-80) REVERT: D 11 PHE cc_start: 0.7966 (p90) cc_final: 0.7027 (p90) REVERT: D 112 PHE cc_start: 0.8195 (m-80) cc_final: 0.7992 (m-10) REVERT: D 121 ARG cc_start: 0.7998 (mtt180) cc_final: 0.7467 (mmp-170) REVERT: E 11 PHE cc_start: 0.5173 (p90) cc_final: 0.4037 (p90) REVERT: E 112 PHE cc_start: 0.6832 (OUTLIER) cc_final: 0.6608 (t80) REVERT: H 105 TYR cc_start: 0.7937 (t80) cc_final: 0.7507 (t80) REVERT: I 105 TYR cc_start: 0.7680 (t80) cc_final: 0.7137 (OUTLIER) outliers start: 31 outliers final: 21 residues processed: 99 average time/residue: 0.2805 time to fit residues: 30.6543 Evaluate side-chains 76 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain C residue 9 ASN Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain E residue 112 PHE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 123 CYS Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 123 CYS Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 88 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 74 optimal weight: 0.0870 overall best weight: 3.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5138 r_free = 0.5138 target = 0.136140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.119058 restraints weight = 34571.957| |-----------------------------------------------------------------------------| r_work (start): 0.4918 rms_B_bonded: 9.06 r_work (final): 0.4918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5986 moved from start: 1.0247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7524 Z= 0.166 Angle : 0.710 12.543 10260 Z= 0.381 Chirality : 0.051 0.198 1260 Planarity : 0.005 0.063 1296 Dihedral : 5.994 35.570 1026 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 20.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.44 % Allowed : 16.95 % Favored : 79.61 % 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: -0.38 (0.28), residues: 927 helix: None (None), residues: 0 sheet: -0.09 (0.23), residues: 486 loop : -0.29 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 121 TYR 0.021 0.002 TYR F 105 PHE 0.022 0.003 PHE C 11 TRP 0.014 0.003 TRP C 39 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 7515) covalent geometry : angle 0.70981 (10242) SS BOND : bond 0.00114 ( 9) SS BOND : angle 0.59968 ( 18) hydrogen bonds : bond 0.03898 ( 392) hydrogen bonds : angle 7.42905 ( 1041) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 TYR cc_start: 0.4709 (t80) cc_final: 0.4014 (t80) REVERT: A 105 TYR cc_start: 0.8220 (t80) cc_final: 0.7663 (t80) REVERT: B 11 PHE cc_start: 0.7810 (p90) cc_final: 0.7560 (p90) REVERT: B 85 TYR cc_start: 0.6811 (t80) cc_final: 0.6554 (t80) REVERT: B 110 TYR cc_start: 0.7881 (p90) cc_final: 0.7618 (p90) REVERT: C 11 PHE cc_start: 0.8088 (p90) cc_final: 0.7736 (p90) REVERT: C 81 ASN cc_start: 0.7940 (p0) cc_final: 0.7589 (p0) REVERT: C 88 PHE cc_start: 0.8759 (m-80) cc_final: 0.8320 (m-80) REVERT: C 113 GLN cc_start: 0.8023 (mt0) cc_final: 0.7727 (mp-120) REVERT: D 10 GLU cc_start: 0.8713 (mp0) cc_final: 0.8391 (mp0) REVERT: D 11 PHE cc_start: 0.8212 (p90) cc_final: 0.7928 (p90) REVERT: D 113 GLN cc_start: 0.7880 (mt0) cc_final: 0.7611 (mt0) REVERT: D 121 ARG cc_start: 0.7857 (mtt180) cc_final: 0.7458 (mmp-170) REVERT: E 112 PHE cc_start: 0.5871 (OUTLIER) cc_final: 0.5209 (t80) REVERT: F 92 SER cc_start: 0.6693 (OUTLIER) cc_final: 0.6480 (m) REVERT: H 105 TYR cc_start: 0.7839 (t80) cc_final: 0.7343 (t80) REVERT: I 105 TYR cc_start: 0.7399 (t80) cc_final: 0.6737 (OUTLIER) outliers start: 30 outliers final: 18 residues processed: 105 average time/residue: 0.2741 time to fit residues: 32.2308 Evaluate side-chains 83 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain C residue 9 ASN Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain E residue 112 PHE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 123 CYS Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain I residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 34 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN H 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.122972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.103809 restraints weight = 32153.806| |-----------------------------------------------------------------------------| r_work (start): 0.4718 rms_B_bonded: 8.95 r_work (final): 0.4718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 moved from start: 1.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7524 Z= 0.237 Angle : 0.810 11.803 10260 Z= 0.442 Chirality : 0.055 0.235 1260 Planarity : 0.005 0.072 1296 Dihedral : 6.877 40.154 1026 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 35.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.58 % Allowed : 17.75 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.27), residues: 927 helix: None (None), residues: 0 sheet: -0.34 (0.25), residues: 432 loop : -0.93 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 109 TYR 0.024 0.003 TYR H 54 PHE 0.035 0.004 PHE A 112 TRP 0.020 0.003 TRP F 39 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 7515) covalent geometry : angle 0.80866 (10242) SS BOND : bond 0.00795 ( 9) SS BOND : angle 1.23343 ( 18) hydrogen bonds : bond 0.04919 ( 392) hydrogen bonds : angle 9.13240 ( 1041) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 92 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 TYR cc_start: 0.6677 (t80) cc_final: 0.6261 (t80) REVERT: B 113 GLN cc_start: 0.8248 (mp-120) cc_final: 0.7820 (mp10) REVERT: B 123 CYS cc_start: 0.6035 (OUTLIER) cc_final: 0.5505 (t) REVERT: C 81 ASN cc_start: 0.8384 (p0) cc_final: 0.7941 (p0) REVERT: C 88 PHE cc_start: 0.8446 (m-80) cc_final: 0.8150 (m-10) REVERT: C 105 TYR cc_start: 0.7289 (t80) cc_final: 0.6972 (t80) REVERT: C 118 LYS cc_start: 0.7906 (tttt) cc_final: 0.6824 (tmtp) REVERT: D 40 LYS cc_start: 0.8815 (pptt) cc_final: 0.8548 (ttpt) REVERT: D 113 GLN cc_start: 0.8083 (mt0) cc_final: 0.7195 (pt0) REVERT: D 121 ARG cc_start: 0.7774 (mtt180) cc_final: 0.7368 (mmp-170) REVERT: F 40 LYS cc_start: 0.8003 (pptt) cc_final: 0.7780 (pmmt) REVERT: H 37 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.8032 (t0) REVERT: H 105 TYR cc_start: 0.7931 (t80) cc_final: 0.7181 (t80) REVERT: I 105 TYR cc_start: 0.7778 (t80) cc_final: 0.7075 (t80) outliers start: 40 outliers final: 19 residues processed: 118 average time/residue: 0.3456 time to fit residues: 44.4519 Evaluate side-chains 93 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain B residue 11 PHE Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 112 PHE Chi-restraints excluded: chain E residue 123 CYS Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain H residue 37 ASN Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain I residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 2 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 89 optimal weight: 9.9990 chunk 1 optimal weight: 30.0000 chunk 17 optimal weight: 4.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 ASN B 66 GLN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.115201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.096079 restraints weight = 32074.133| |-----------------------------------------------------------------------------| r_work (start): 0.4617 rms_B_bonded: 8.70 r_work (final): 0.4617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 1.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 7524 Z= 0.265 Angle : 0.861 12.030 10260 Z= 0.470 Chirality : 0.058 0.310 1260 Planarity : 0.006 0.088 1296 Dihedral : 7.161 36.274 1026 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 39.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.89 % Allowed : 21.76 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.27), residues: 927 helix: None (None), residues: 0 sheet: -0.58 (0.26), residues: 396 loop : -1.26 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 109 TYR 0.024 0.003 TYR H 85 PHE 0.042 0.004 PHE A 112 TRP 0.018 0.004 TRP F 39 Details of bonding type rmsd covalent geometry : bond 0.00575 ( 7515) covalent geometry : angle 0.86023 (10242) SS BOND : bond 0.00564 ( 9) SS BOND : angle 1.07005 ( 18) hydrogen bonds : bond 0.05282 ( 392) hydrogen bonds : angle 9.83043 ( 1041) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.7954 (p0) REVERT: B 123 CYS cc_start: 0.6606 (OUTLIER) cc_final: 0.6330 (t) REVERT: C 50 THR cc_start: 0.7832 (OUTLIER) cc_final: 0.7347 (p) REVERT: C 113 GLN cc_start: 0.8474 (mp-120) cc_final: 0.7257 (mp10) REVERT: C 118 LYS cc_start: 0.8212 (tttt) cc_final: 0.7092 (tmtp) REVERT: D 40 LYS cc_start: 0.8839 (pptt) cc_final: 0.8372 (tptm) REVERT: D 61 ASN cc_start: 0.5884 (m110) cc_final: 0.5609 (m110) REVERT: D 90 LEU cc_start: 0.9106 (mm) cc_final: 0.8287 (tp) REVERT: D 112 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.6754 (m-10) REVERT: D 121 ARG cc_start: 0.8126 (mtt180) cc_final: 0.7497 (mmp-170) REVERT: F 10 GLU cc_start: 0.4945 (pm20) cc_final: 0.4440 (pm20) REVERT: F 40 LYS cc_start: 0.7867 (pptt) cc_final: 0.7594 (pmmt) REVERT: F 105 TYR cc_start: 0.7709 (t80) cc_final: 0.7428 (t80) REVERT: G 66 GLN cc_start: 0.7556 (pt0) cc_final: 0.7162 (mp10) REVERT: I 56 ASN cc_start: 0.6824 (t0) cc_final: 0.5547 (p0) outliers start: 34 outliers final: 17 residues processed: 118 average time/residue: 0.3255 time to fit residues: 42.2704 Evaluate side-chains 92 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 111 CYS Chi-restraints excluded: chain D residue 112 PHE Chi-restraints excluded: chain E residue 123 CYS Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain I residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 30.0000 chunk 87 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN D 113 GLN ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN ** G 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 GLN H 37 ASN H 73 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5013 r_free = 0.5013 target = 0.126018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.105660 restraints weight = 27718.053| |-----------------------------------------------------------------------------| r_work (start): 0.4714 rms_B_bonded: 8.52 r_work (final): 0.4714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 1.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7524 Z= 0.162 Angle : 0.802 14.123 10260 Z= 0.427 Chirality : 0.055 0.263 1260 Planarity : 0.004 0.067 1296 Dihedral : 6.269 37.863 1026 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 23.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.32 % Allowed : 23.83 % Favored : 72.85 % 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: -0.99 (0.28), residues: 927 helix: None (None), residues: 0 sheet: -0.61 (0.23), residues: 495 loop : -0.53 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 109 TYR 0.022 0.002 TYR C 85 PHE 0.024 0.003 PHE B 88 TRP 0.017 0.002 TRP F 39 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 7515) covalent geometry : angle 0.80148 (10242) SS BOND : bond 0.00226 ( 9) SS BOND : angle 0.97379 ( 18) hydrogen bonds : bond 0.04002 ( 392) hydrogen bonds : angle 8.07263 ( 1041) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 15 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7587 (mp) REVERT: B 123 CYS cc_start: 0.6549 (OUTLIER) cc_final: 0.6274 (t) REVERT: C 56 ASN cc_start: 0.7445 (t0) cc_final: 0.6946 (t0) REVERT: C 90 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7731 (mm) REVERT: C 105 TYR cc_start: 0.6794 (t80) cc_final: 0.6485 (t80) REVERT: C 113 GLN cc_start: 0.8398 (mp-120) cc_final: 0.8122 (mp10) REVERT: D 11 PHE cc_start: 0.7749 (p90) cc_final: 0.7319 (p90) REVERT: D 40 LYS cc_start: 0.8672 (pptt) cc_final: 0.8382 (ttpt) REVERT: D 50 THR cc_start: 0.6883 (p) cc_final: 0.6437 (t) REVERT: D 121 ARG cc_start: 0.8082 (mtt180) cc_final: 0.7476 (mmp-170) REVERT: E 11 PHE cc_start: 0.5475 (p90) cc_final: 0.4975 (p90) REVERT: E 51 ILE cc_start: 0.6824 (pp) cc_final: 0.6214 (mm) REVERT: F 10 GLU cc_start: 0.4198 (pm20) cc_final: 0.3669 (mp0) REVERT: F 40 LYS cc_start: 0.7716 (pptt) cc_final: 0.7230 (pmmt) REVERT: G 66 GLN cc_start: 0.7276 (pt0) cc_final: 0.7047 (mp10) REVERT: H 37 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.7443 (t0) REVERT: H 105 TYR cc_start: 0.7760 (t80) cc_final: 0.7158 (t80) REVERT: I 56 ASN cc_start: 0.6490 (t0) cc_final: 0.5222 (m110) REVERT: I 105 TYR cc_start: 0.7249 (t80) cc_final: 0.6830 (t80) outliers start: 29 outliers final: 14 residues processed: 116 average time/residue: 0.2824 time to fit residues: 36.1513 Evaluate side-chains 91 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 9 ASN Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain E residue 123 CYS Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain H residue 37 ASN Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain I residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 58 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 21 optimal weight: 30.0000 chunk 50 optimal weight: 8.9990 chunk 1 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN ** G 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4953 r_free = 0.4953 target = 0.120938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.101065 restraints weight = 28292.676| |-----------------------------------------------------------------------------| r_work (start): 0.4656 rms_B_bonded: 8.25 r_work (final): 0.4656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 1.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7524 Z= 0.216 Angle : 0.854 14.605 10260 Z= 0.457 Chirality : 0.056 0.239 1260 Planarity : 0.005 0.074 1296 Dihedral : 6.737 34.738 1026 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 35.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.21 % Allowed : 25.43 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.28), residues: 927 helix: None (None), residues: 0 sheet: -0.64 (0.24), residues: 477 loop : -0.77 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 121 TYR 0.024 0.003 TYR C 85 PHE 0.027 0.003 PHE C 88 TRP 0.018 0.003 TRP C 39 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 7515) covalent geometry : angle 0.85374 (10242) SS BOND : bond 0.00292 ( 9) SS BOND : angle 0.78640 ( 18) hydrogen bonds : bond 0.04507 ( 392) hydrogen bonds : angle 8.95217 ( 1041) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.8514 (mp0) cc_final: 0.8268 (mp0) REVERT: B 51 ILE cc_start: 0.8554 (mt) cc_final: 0.8215 (mp) REVERT: D 38 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7304 (mp) REVERT: D 40 LYS cc_start: 0.8763 (pptt) cc_final: 0.8425 (ttpt) REVERT: D 121 ARG cc_start: 0.8272 (mtt180) cc_final: 0.7533 (mmp-170) REVERT: E 17 ILE cc_start: 0.5461 (mt) cc_final: 0.5233 (mp) REVERT: F 40 LYS cc_start: 0.7858 (pptt) cc_final: 0.7591 (pmmt) REVERT: G 66 GLN cc_start: 0.7300 (pt0) cc_final: 0.7015 (mp10) REVERT: H 37 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.7700 (t0) REVERT: I 105 TYR cc_start: 0.7500 (t80) cc_final: 0.7094 (t80) outliers start: 28 outliers final: 15 residues processed: 105 average time/residue: 0.2492 time to fit residues: 29.2461 Evaluate side-chains 91 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain E residue 123 CYS Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 73 ASN Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain H residue 37 ASN Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain I residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 50 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 38 optimal weight: 0.0470 chunk 77 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 overall best weight: 3.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 ASN D 9 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN ** G 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** G 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4963 r_free = 0.4963 target = 0.122351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.103067 restraints weight = 27449.515| |-----------------------------------------------------------------------------| r_work (start): 0.4687 rms_B_bonded: 8.03 r_work (final): 0.4687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 moved from start: 1.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7524 Z= 0.180 Angle : 0.844 14.503 10260 Z= 0.445 Chirality : 0.055 0.293 1260 Planarity : 0.005 0.072 1296 Dihedral : 6.394 35.981 1026 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 29.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.86 % Allowed : 26.58 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.28), residues: 927 helix: None (None), residues: 0 sheet: -0.75 (0.23), residues: 495 loop : -0.55 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 121 TYR 0.027 0.002 TYR B 110 PHE 0.027 0.003 PHE B 11 TRP 0.017 0.003 TRP F 39 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 7515) covalent geometry : angle 0.84332 (10242) SS BOND : bond 0.00240 ( 9) SS BOND : angle 1.34122 ( 18) hydrogen bonds : bond 0.03942 ( 392) hydrogen bonds : angle 8.24524 ( 1041) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 110 TYR cc_start: 0.8246 (p90) cc_final: 0.8041 (p90) REVERT: B 51 ILE cc_start: 0.8522 (mt) cc_final: 0.8245 (mp) REVERT: B 81 ASN cc_start: 0.7593 (p0) cc_final: 0.7370 (p0) REVERT: C 81 ASN cc_start: 0.7515 (OUTLIER) cc_final: 0.7294 (p0) REVERT: D 40 LYS cc_start: 0.8744 (pptt) cc_final: 0.8512 (ttpt) REVERT: D 113 GLN cc_start: 0.8054 (mt0) cc_final: 0.7600 (pt0) REVERT: D 121 ARG cc_start: 0.8176 (mtt180) cc_final: 0.7483 (mmp-170) REVERT: F 40 LYS cc_start: 0.7522 (pptt) cc_final: 0.7299 (pmmt) REVERT: G 66 GLN cc_start: 0.7299 (pt0) cc_final: 0.6973 (mp10) REVERT: H 37 ASN cc_start: 0.8553 (OUTLIER) cc_final: 0.7799 (t0) REVERT: H 105 TYR cc_start: 0.7737 (t80) cc_final: 0.7131 (t80) REVERT: I 56 ASN cc_start: 0.6681 (t0) cc_final: 0.5393 (m110) outliers start: 25 outliers final: 13 residues processed: 106 average time/residue: 0.2305 time to fit residues: 27.5720 Evaluate side-chains 93 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain E residue 123 CYS Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 73 ASN Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain H residue 37 ASN Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain I residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 21 optimal weight: 30.0000 chunk 32 optimal weight: 0.9990 chunk 81 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 22 optimal weight: 0.0670 chunk 68 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN ** G 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4954 r_free = 0.4954 target = 0.121437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.101658 restraints weight = 27414.321| |-----------------------------------------------------------------------------| r_work (start): 0.4671 rms_B_bonded: 8.31 r_work (final): 0.4671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 1.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7524 Z= 0.185 Angle : 0.851 14.304 10260 Z= 0.448 Chirality : 0.055 0.280 1260 Planarity : 0.004 0.065 1296 Dihedral : 6.413 32.018 1026 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 30.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.86 % Allowed : 27.03 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.28), residues: 927 helix: None (None), residues: 0 sheet: -0.77 (0.23), residues: 495 loop : -0.60 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 121 TYR 0.023 0.002 TYR B 110 PHE 0.025 0.003 PHE B 11 TRP 0.018 0.003 TRP B 39 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 7515) covalent geometry : angle 0.85042 (10242) SS BOND : bond 0.00228 ( 9) SS BOND : angle 1.12115 ( 18) hydrogen bonds : bond 0.03940 ( 392) hydrogen bonds : angle 8.19944 ( 1041) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2082.16 seconds wall clock time: 36 minutes 42.58 seconds (2202.58 seconds total)