Starting phenix.real_space_refine on Thu Feb 5 23:22:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kms_62443/02_2026/9kms_62443.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kms_62443/02_2026/9kms_62443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kms_62443/02_2026/9kms_62443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kms_62443/02_2026/9kms_62443.map" model { file = "/net/cci-nas-00/data/ceres_data/9kms_62443/02_2026/9kms_62443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kms_62443/02_2026/9kms_62443.cif" } resolution = 4.2 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= 0.026 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: 5 Type Number sf(0) Gaussians S 35 5.16 5 C 8170 2.51 5 N 2140 2.21 5 O 2420 1.98 5 H 7960 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 20725 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "D" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 921 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Restraints were copied for chains: A, E, G, I, B, F, H, J Time building chain proxies: 3.32, per 1000 atoms: 0.16 Number of scatterers: 20725 At special positions: 0 Unit cell: (108.94, 109.778, 75.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 35 16.00 O 2420 8.00 N 2140 7.00 C 8170 6.00 H 7960 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 97 " distance=2.43 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 97 " distance=2.43 Simple disulfide: pdb=" SG CYS E 36 " - pdb=" SG CYS E 97 " distance=2.43 Simple disulfide: pdb=" SG CYS G 36 " - pdb=" SG CYS G 97 " distance=2.43 Simple disulfide: pdb=" SG CYS I 36 " - pdb=" SG CYS I 97 " distance=2.43 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 700.2 milliseconds 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 25 sheets defined 10.8% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'C' and resid 42 through 46 removed outlier: 3.523A pdb=" N SER C 45 " --> pdb=" O GLU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'C' and resid 186 through 190 removed outlier: 3.598A pdb=" N LEU C 190 " --> pdb=" O TRP C 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 33 Processing helix chain 'D' and resid 63 through 66 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.523A pdb=" N SER A 45 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 177 Processing helix chain 'A' and resid 186 through 190 removed outlier: 3.598A pdb=" N LEU A 190 " --> pdb=" O TRP A 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 33 Processing helix chain 'B' and resid 63 through 66 Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'E' and resid 42 through 46 removed outlier: 3.523A pdb=" N SER E 45 " --> pdb=" O GLU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 177 Processing helix chain 'E' and resid 186 through 190 removed outlier: 3.598A pdb=" N LEU E 190 " --> pdb=" O TRP E 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 33 Processing helix chain 'F' and resid 63 through 66 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'G' and resid 42 through 46 removed outlier: 3.523A pdb=" N SER G 45 " --> pdb=" O GLU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 177 Processing helix chain 'G' and resid 186 through 190 removed outlier: 3.597A pdb=" N LEU G 190 " --> pdb=" O TRP G 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 33 Processing helix chain 'H' and resid 63 through 66 Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'I' and resid 42 through 46 removed outlier: 3.523A pdb=" N SER I 45 " --> pdb=" O GLU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 177 Processing helix chain 'I' and resid 186 through 190 removed outlier: 3.598A pdb=" N LEU I 190 " --> pdb=" O TRP I 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 33 Processing helix chain 'J' and resid 63 through 66 Processing helix chain 'J' and resid 88 through 92 Processing sheet with id=AA1, first strand: chain 'C' and resid 110 through 111 removed outlier: 4.528A pdb=" N HIS C 38 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ASN C 158 " --> pdb=" O HIS C 38 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N TYR C 40 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ILE C 156 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 19 through 23 removed outlier: 4.552A pdb=" N LYS C 191 " --> pdb=" O LYS C 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 50 through 54 removed outlier: 6.400A pdb=" N SER C 50 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP C 67 " --> pdb=" O SER C 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 12 through 15 removed outlier: 3.935A pdb=" N ILE D 94 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE D 100 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL D 36 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LEU D 52 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP D 38 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP D 48 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 20 through 24 Processing sheet with id=AA6, first strand: chain 'A' and resid 110 through 111 removed outlier: 4.528A pdb=" N HIS A 38 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASN A 158 " --> pdb=" O HIS A 38 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TYR A 40 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ILE A 156 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 19 through 23 removed outlier: 4.552A pdb=" N LYS A 191 " --> pdb=" O LYS A 23 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 50 through 54 removed outlier: 6.400A pdb=" N SER A 50 " --> pdb=" O TRP A 67 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP A 67 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 12 through 15 removed outlier: 3.934A pdb=" N ILE B 94 " --> pdb=" O GLN B 41 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE B 100 " --> pdb=" O THR B 35 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL B 36 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LEU B 52 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP B 38 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 48 " --> pdb=" O ARG B 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 20 through 24 Processing sheet with id=AB2, first strand: chain 'E' and resid 110 through 111 removed outlier: 4.528A pdb=" N HIS E 38 " --> pdb=" O ASN E 158 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASN E 158 " --> pdb=" O HIS E 38 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N TYR E 40 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ILE E 156 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 19 through 23 removed outlier: 4.552A pdb=" N LYS E 191 " --> pdb=" O LYS E 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 50 through 54 removed outlier: 6.399A pdb=" N SER E 50 " --> pdb=" O TRP E 67 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP E 67 " --> pdb=" O SER E 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 12 through 15 removed outlier: 3.935A pdb=" N ILE F 94 " --> pdb=" O GLN F 41 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE F 100 " --> pdb=" O THR F 35 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL F 36 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU F 52 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP F 38 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP F 48 " --> pdb=" O ARG F 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 20 through 24 Processing sheet with id=AB7, first strand: chain 'G' and resid 110 through 111 removed outlier: 4.528A pdb=" N HIS G 38 " --> pdb=" O ASN G 158 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ASN G 158 " --> pdb=" O HIS G 38 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TYR G 40 " --> pdb=" O ILE G 156 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ILE G 156 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 19 through 23 removed outlier: 4.552A pdb=" N LYS G 191 " --> pdb=" O LYS G 23 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 50 through 54 removed outlier: 6.400A pdb=" N SER G 50 " --> pdb=" O TRP G 67 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP G 67 " --> pdb=" O SER G 50 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 12 through 15 removed outlier: 3.935A pdb=" N ILE H 94 " --> pdb=" O GLN H 41 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE H 100 " --> pdb=" O THR H 35 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL H 36 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LEU H 52 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP H 38 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP H 48 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 20 through 24 Processing sheet with id=AC3, first strand: chain 'I' and resid 110 through 111 removed outlier: 4.528A pdb=" N HIS I 38 " --> pdb=" O ASN I 158 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASN I 158 " --> pdb=" O HIS I 38 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TYR I 40 " --> pdb=" O ILE I 156 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ILE I 156 " --> pdb=" O TYR I 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 19 through 23 removed outlier: 4.552A pdb=" N LYS I 191 " --> pdb=" O LYS I 23 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 50 through 54 removed outlier: 6.400A pdb=" N SER I 50 " --> pdb=" O TRP I 67 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP I 67 " --> pdb=" O SER I 50 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 12 through 15 removed outlier: 3.934A pdb=" N ILE J 94 " --> pdb=" O GLN J 41 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE J 100 " --> pdb=" O THR J 35 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL J 36 " --> pdb=" O LEU J 52 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LEU J 52 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP J 38 " --> pdb=" O VAL J 50 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP J 48 " --> pdb=" O ARG J 40 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 20 through 24 405 hydrogen bonds defined for protein. 885 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: 4.82 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 7960 1.02 - 1.21: 20 1.21 - 1.41: 5530 1.41 - 1.61: 7485 1.61 - 1.81: 50 Bond restraints: 21045 Sorted by residual: bond pdb=" C GLU I 85 " pdb=" N VAL I 86 " ideal model delta sigma weight residual 1.330 1.444 -0.114 8.40e-03 1.42e+04 1.85e+02 bond pdb=" C GLU C 85 " pdb=" N VAL C 86 " ideal model delta sigma weight residual 1.330 1.444 -0.114 8.40e-03 1.42e+04 1.84e+02 bond pdb=" C GLU E 85 " pdb=" N VAL E 86 " ideal model delta sigma weight residual 1.330 1.444 -0.114 8.40e-03 1.42e+04 1.83e+02 bond pdb=" C GLU A 85 " pdb=" N VAL A 86 " ideal model delta sigma weight residual 1.330 1.443 -0.113 8.40e-03 1.42e+04 1.81e+02 bond pdb=" C GLU G 85 " pdb=" N VAL G 86 " ideal model delta sigma weight residual 1.330 1.443 -0.113 8.40e-03 1.42e+04 1.81e+02 ... (remaining 21040 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 34607 2.20 - 4.39: 1006 4.39 - 6.59: 162 6.59 - 8.79: 78 8.79 - 10.98: 32 Bond angle restraints: 35885 Sorted by residual: angle pdb=" C GLU E 85 " pdb=" N VAL E 86 " pdb=" CA VAL E 86 " ideal model delta sigma weight residual 122.85 115.01 7.84 1.14e+00 7.69e-01 4.73e+01 angle pdb=" C GLU C 85 " pdb=" N VAL C 86 " pdb=" CA VAL C 86 " ideal model delta sigma weight residual 122.85 115.04 7.81 1.14e+00 7.69e-01 4.69e+01 angle pdb=" C GLU G 85 " pdb=" N VAL G 86 " pdb=" CA VAL G 86 " ideal model delta sigma weight residual 122.85 115.05 7.80 1.14e+00 7.69e-01 4.69e+01 angle pdb=" C GLU I 85 " pdb=" N VAL I 86 " pdb=" CA VAL I 86 " ideal model delta sigma weight residual 122.85 115.07 7.78 1.14e+00 7.69e-01 4.66e+01 angle pdb=" C GLU A 85 " pdb=" N VAL A 86 " pdb=" CA VAL A 86 " ideal model delta sigma weight residual 122.85 115.08 7.77 1.14e+00 7.69e-01 4.65e+01 ... (remaining 35880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.40: 9035 16.40 - 32.81: 1004 32.81 - 49.21: 306 49.21 - 65.61: 130 65.61 - 82.02: 35 Dihedral angle restraints: 10510 sinusoidal: 5140 harmonic: 5370 Sorted by residual: dihedral pdb=" C ILE C 71 " pdb=" N ILE C 71 " pdb=" CA ILE C 71 " pdb=" CB ILE C 71 " ideal model delta harmonic sigma weight residual -122.00 -136.45 14.45 0 2.50e+00 1.60e-01 3.34e+01 dihedral pdb=" C ILE G 71 " pdb=" N ILE G 71 " pdb=" CA ILE G 71 " pdb=" CB ILE G 71 " ideal model delta harmonic sigma weight residual -122.00 -136.38 14.38 0 2.50e+00 1.60e-01 3.31e+01 dihedral pdb=" C ILE A 71 " pdb=" N ILE A 71 " pdb=" CA ILE A 71 " pdb=" CB ILE A 71 " ideal model delta harmonic sigma weight residual -122.00 -136.36 14.36 0 2.50e+00 1.60e-01 3.30e+01 ... (remaining 10507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1617 0.081 - 0.163: 260 0.163 - 0.244: 43 0.244 - 0.325: 5 0.325 - 0.407: 10 Chirality restraints: 1935 Sorted by residual: chirality pdb=" CA ILE C 71 " pdb=" N ILE C 71 " pdb=" C ILE C 71 " pdb=" CB ILE C 71 " both_signs ideal model delta sigma weight residual False 2.43 2.03 0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CA ILE A 71 " pdb=" N ILE A 71 " pdb=" C ILE A 71 " pdb=" CB ILE A 71 " both_signs ideal model delta sigma weight residual False 2.43 2.03 0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CA ILE E 71 " pdb=" N ILE E 71 " pdb=" C ILE E 71 " pdb=" CB ILE E 71 " both_signs ideal model delta sigma weight residual False 2.43 2.03 0.40 2.00e-01 2.50e+01 4.04e+00 ... (remaining 1932 not shown) Planarity restraints: 3235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN I 145 " -0.317 2.00e-02 2.50e+03 3.97e-01 2.36e+03 pdb=" CG ASN I 145 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN I 145 " 0.309 2.00e-02 2.50e+03 pdb=" ND2 ASN I 145 " 0.005 2.00e-02 2.50e+03 pdb="HD21 ASN I 145 " 0.601 2.00e-02 2.50e+03 pdb="HD22 ASN I 145 " -0.621 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 145 " -0.318 2.00e-02 2.50e+03 3.97e-01 2.36e+03 pdb=" CG ASN G 145 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN G 145 " 0.309 2.00e-02 2.50e+03 pdb=" ND2 ASN G 145 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN G 145 " 0.601 2.00e-02 2.50e+03 pdb="HD22 ASN G 145 " -0.621 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 145 " -0.317 2.00e-02 2.50e+03 3.96e-01 2.36e+03 pdb=" CG ASN C 145 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN C 145 " 0.309 2.00e-02 2.50e+03 pdb=" ND2 ASN C 145 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN C 145 " 0.601 2.00e-02 2.50e+03 pdb="HD22 ASN C 145 " -0.621 2.00e-02 2.50e+03 ... (remaining 3232 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 1967 2.19 - 2.79: 37870 2.79 - 3.40: 59273 3.40 - 4.00: 80826 4.00 - 4.60: 117717 Nonbonded interactions: 297653 Sorted by model distance: nonbonded pdb=" OE1 GLU C 14 " pdb=" H GLU C 14 " model vdw 1.591 2.450 nonbonded pdb=" OE1 GLU I 14 " pdb=" H GLU I 14 " model vdw 1.592 2.450 nonbonded pdb=" OE1 GLU G 14 " pdb=" H GLU G 14 " model vdw 1.593 2.450 nonbonded pdb=" OE1 GLU E 14 " pdb=" H GLU E 14 " model vdw 1.593 2.450 nonbonded pdb=" OE1 GLU A 14 " pdb=" H GLU A 14 " model vdw 1.593 2.450 ... (remaining 297648 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: 0.05 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' selection = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'B' selection = chain 'F' selection = chain 'H' selection = chain 'J' } 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: 1.360 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: 0.160 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.640 Find NCS groups from input model: 0.150 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.010 0.398 13090 Z= 0.632 Angle : 1.204 15.762 17770 Z= 0.761 Chirality : 0.066 0.407 1935 Planarity : 0.006 0.037 2265 Dihedral : 14.049 80.072 4655 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 68.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.58 % Allowed : 14.53 % Favored : 84.89 % Cbeta Deviations : 0.34 % 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: -3.51 (0.18), residues: 1605 helix: 0.85 (0.54), residues: 55 sheet: -3.10 (0.19), residues: 540 loop : -2.09 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 118 TYR 0.023 0.002 TYR C 54 PHE 0.048 0.004 PHE C 109 TRP 0.009 0.001 TRP F 38 HIS 0.003 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00672 (13085) covalent geometry : angle 1.17360 (17760) SS BOND : bond 0.39754 ( 5) SS BOND : angle 11.34386 ( 10) hydrogen bonds : bond 0.14325 ( 405) hydrogen bonds : angle 8.60910 ( 885) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 721 time to evaluate : 0.622 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 THR cc_start: 0.9199 (m) cc_final: 0.8905 (m) REVERT: C 36 CYS cc_start: 0.7994 (m) cc_final: 0.7775 (m) REVERT: C 85 GLU cc_start: 0.9164 (tt0) cc_final: 0.8710 (tm-30) REVERT: C 95 HIS cc_start: 0.8731 (t-90) cc_final: 0.7785 (t70) REVERT: C 112 ASP cc_start: 0.8962 (t0) cc_final: 0.8759 (t0) REVERT: C 130 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8777 (pp20) REVERT: C 135 LEU cc_start: 0.9099 (mp) cc_final: 0.8857 (mp) REVERT: C 163 ASP cc_start: 0.9186 (p0) cc_final: 0.8885 (p0) REVERT: C 175 TYR cc_start: 0.9100 (t80) cc_final: 0.8814 (t80) REVERT: D 34 TYR cc_start: 0.7909 (m-10) cc_final: 0.7571 (m-10) REVERT: D 38 TRP cc_start: 0.9424 (m100) cc_final: 0.8731 (m100) REVERT: D 48 ASP cc_start: 0.9219 (t70) cc_final: 0.8991 (t70) REVERT: D 110 TYR cc_start: 0.8353 (m-80) cc_final: 0.7930 (m-80) REVERT: A 34 THR cc_start: 0.9161 (m) cc_final: 0.8885 (m) REVERT: A 36 CYS cc_start: 0.7914 (m) cc_final: 0.7673 (m) REVERT: A 85 GLU cc_start: 0.9119 (tt0) cc_final: 0.8660 (tm-30) REVERT: A 95 HIS cc_start: 0.8736 (t-90) cc_final: 0.8309 (t-170) REVERT: A 130 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8763 (pp20) REVERT: A 163 ASP cc_start: 0.9230 (p0) cc_final: 0.8942 (p0) REVERT: B 19 SER cc_start: 0.8562 (m) cc_final: 0.8121 (m) REVERT: B 38 TRP cc_start: 0.9398 (m100) cc_final: 0.8703 (m100) REVERT: B 48 ASP cc_start: 0.9171 (t70) cc_final: 0.8932 (t70) REVERT: B 91 ASP cc_start: 0.8050 (m-30) cc_final: 0.7791 (m-30) REVERT: E 34 THR cc_start: 0.9174 (m) cc_final: 0.8943 (m) REVERT: E 36 CYS cc_start: 0.8073 (m) cc_final: 0.7791 (m) REVERT: E 85 GLU cc_start: 0.9120 (tt0) cc_final: 0.8661 (tm-30) REVERT: E 95 HIS cc_start: 0.8735 (t-90) cc_final: 0.7783 (t70) REVERT: E 130 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8751 (pp20) REVERT: E 163 ASP cc_start: 0.9172 (p0) cc_final: 0.8870 (p0) REVERT: F 19 SER cc_start: 0.8472 (m) cc_final: 0.8007 (m) REVERT: F 34 TYR cc_start: 0.7829 (m-10) cc_final: 0.7467 (m-10) REVERT: F 38 TRP cc_start: 0.9416 (m100) cc_final: 0.8735 (m100) REVERT: F 73 ARG cc_start: 0.7719 (ttm-80) cc_final: 0.7516 (ttm170) REVERT: F 91 ASP cc_start: 0.8123 (m-30) cc_final: 0.7824 (m-30) REVERT: F 110 TYR cc_start: 0.8384 (m-80) cc_final: 0.8049 (m-80) REVERT: G 34 THR cc_start: 0.9153 (m) cc_final: 0.8931 (m) REVERT: G 85 GLU cc_start: 0.9130 (tt0) cc_final: 0.8604 (tm-30) REVERT: G 130 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8659 (pp20) REVERT: G 135 LEU cc_start: 0.9174 (mp) cc_final: 0.8964 (mp) REVERT: G 163 ASP cc_start: 0.9211 (p0) cc_final: 0.8947 (p0) REVERT: H 38 TRP cc_start: 0.9432 (m100) cc_final: 0.8751 (m100) REVERT: H 91 ASP cc_start: 0.8049 (m-30) cc_final: 0.7708 (m-30) REVERT: I 34 THR cc_start: 0.9164 (m) cc_final: 0.8871 (m) REVERT: I 36 CYS cc_start: 0.8103 (m) cc_final: 0.7883 (m) REVERT: I 73 TYR cc_start: 0.9422 (m-80) cc_final: 0.9211 (m-80) REVERT: I 85 GLU cc_start: 0.9116 (tt0) cc_final: 0.8642 (tm-30) REVERT: I 95 HIS cc_start: 0.8730 (t-90) cc_final: 0.7951 (t-170) REVERT: I 108 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8046 (mm-30) REVERT: I 130 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8706 (pp20) REVERT: I 163 ASP cc_start: 0.9198 (p0) cc_final: 0.8937 (p0) REVERT: J 34 TYR cc_start: 0.7792 (m-10) cc_final: 0.7487 (m-10) REVERT: J 38 TRP cc_start: 0.9430 (m100) cc_final: 0.8782 (m100) REVERT: J 73 ARG cc_start: 0.7682 (ttm-80) cc_final: 0.7458 (ttm170) REVERT: J 91 ASP cc_start: 0.8065 (m-30) cc_final: 0.7776 (m-30) REVERT: J 110 TYR cc_start: 0.8356 (m-80) cc_final: 0.8015 (m-80) outliers start: 8 outliers final: 8 residues processed: 721 average time/residue: 0.2054 time to fit residues: 217.2004 Evaluate side-chains 663 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 655 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN D 85 ASN ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.070899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.055509 restraints weight = 89977.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.059472 restraints weight = 33961.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.062138 restraints weight = 16880.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.063941 restraints weight = 9661.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.065087 restraints weight = 6024.496| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13090 Z= 0.217 Angle : 0.607 4.779 17770 Z= 0.341 Chirality : 0.045 0.146 1935 Planarity : 0.004 0.030 2265 Dihedral : 4.961 17.583 1770 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 54.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % 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 : 0.00 % 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: -3.42 (0.18), residues: 1605 helix: 1.95 (0.59), residues: 55 sheet: -2.81 (0.21), residues: 520 loop : -2.29 (0.16), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 118 TYR 0.021 0.002 TYR G 40 PHE 0.024 0.002 PHE C 84 TRP 0.010 0.001 TRP H 38 HIS 0.008 0.002 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00456 (13085) covalent geometry : angle 0.60621 (17760) SS BOND : bond 0.00569 ( 5) SS BOND : angle 1.72471 ( 10) hydrogen bonds : bond 0.04336 ( 405) hydrogen bonds : angle 8.05015 ( 885) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 684 time to evaluate : 0.673 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 THR cc_start: 0.9149 (m) cc_final: 0.8829 (m) REVERT: C 42 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8136 (tm-30) REVERT: C 57 LYS cc_start: 0.9492 (mmmm) cc_final: 0.9166 (mmmm) REVERT: C 85 GLU cc_start: 0.9108 (tt0) cc_final: 0.8667 (tm-30) REVERT: C 95 HIS cc_start: 0.8698 (t-90) cc_final: 0.8159 (t-170) REVERT: C 150 GLN cc_start: 0.9074 (mt0) cc_final: 0.8627 (mt0) REVERT: C 155 ASP cc_start: 0.8776 (p0) cc_final: 0.8525 (p0) REVERT: D 20 LEU cc_start: 0.9447 (tp) cc_final: 0.9210 (tp) REVERT: D 22 LEU cc_start: 0.9624 (mt) cc_final: 0.9406 (mt) REVERT: D 33 ARG cc_start: 0.9035 (ptm-80) cc_final: 0.8798 (ptm-80) REVERT: D 35 THR cc_start: 0.9211 (m) cc_final: 0.8839 (m) REVERT: D 38 TRP cc_start: 0.9044 (m100) cc_final: 0.8302 (m100) REVERT: D 48 ASP cc_start: 0.9148 (t70) cc_final: 0.8683 (p0) REVERT: D 82 LEU cc_start: 0.8800 (tp) cc_final: 0.8424 (tp) REVERT: D 100 PHE cc_start: 0.8559 (p90) cc_final: 0.8265 (p90) REVERT: A 34 THR cc_start: 0.9181 (m) cc_final: 0.8953 (m) REVERT: A 42 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8183 (tm-30) REVERT: A 85 GLU cc_start: 0.9097 (tt0) cc_final: 0.8680 (tm-30) REVERT: A 155 ASP cc_start: 0.8698 (p0) cc_final: 0.8461 (p0) REVERT: B 22 LEU cc_start: 0.9635 (mt) cc_final: 0.9403 (mt) REVERT: B 33 ARG cc_start: 0.8981 (ptm-80) cc_final: 0.8654 (ptm-80) REVERT: B 35 THR cc_start: 0.9325 (m) cc_final: 0.8961 (m) REVERT: B 38 TRP cc_start: 0.9090 (m100) cc_final: 0.8373 (m100) REVERT: B 82 LEU cc_start: 0.8809 (tp) cc_final: 0.8398 (tp) REVERT: B 83 GLN cc_start: 0.9424 (tp40) cc_final: 0.9108 (tp40) REVERT: B 100 PHE cc_start: 0.8601 (p90) cc_final: 0.8391 (p90) REVERT: B 101 ARG cc_start: 0.8230 (ptt180) cc_final: 0.7880 (ptt180) REVERT: E 34 THR cc_start: 0.9157 (m) cc_final: 0.8892 (m) REVERT: E 42 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8171 (tm-30) REVERT: E 57 LYS cc_start: 0.9506 (mmmm) cc_final: 0.9089 (mmmm) REVERT: E 85 GLU cc_start: 0.9004 (tt0) cc_final: 0.8632 (tm-30) REVERT: E 95 HIS cc_start: 0.8684 (t-90) cc_final: 0.8344 (t-170) REVERT: E 109 PHE cc_start: 0.8978 (t80) cc_final: 0.8555 (t80) REVERT: E 150 GLN cc_start: 0.8969 (mt0) cc_final: 0.8588 (mt0) REVERT: E 163 ASP cc_start: 0.9158 (p0) cc_final: 0.8779 (p0) REVERT: F 22 LEU cc_start: 0.9612 (mt) cc_final: 0.9408 (mt) REVERT: F 34 TYR cc_start: 0.7651 (m-10) cc_final: 0.7366 (m-10) REVERT: F 38 TRP cc_start: 0.8984 (m100) cc_final: 0.8144 (m100) REVERT: F 48 ASP cc_start: 0.8959 (t70) cc_final: 0.8601 (p0) REVERT: F 73 ARG cc_start: 0.7762 (ttm-80) cc_final: 0.7370 (ttm170) REVERT: F 82 LEU cc_start: 0.8746 (tp) cc_final: 0.8299 (tp) REVERT: F 83 GLN cc_start: 0.9390 (tp40) cc_final: 0.9086 (tp40) REVERT: G 34 THR cc_start: 0.9163 (m) cc_final: 0.8940 (m) REVERT: G 42 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8176 (tm-30) REVERT: G 57 LYS cc_start: 0.9516 (mmmm) cc_final: 0.9078 (mmmm) REVERT: G 85 GLU cc_start: 0.9086 (tt0) cc_final: 0.8572 (tm-30) REVERT: G 95 HIS cc_start: 0.8869 (t-170) cc_final: 0.8489 (t-170) REVERT: G 150 GLN cc_start: 0.9055 (mt0) cc_final: 0.8604 (mt0) REVERT: H 22 LEU cc_start: 0.9600 (mt) cc_final: 0.9321 (mt) REVERT: H 33 ARG cc_start: 0.9051 (ptm-80) cc_final: 0.8792 (ptm-80) REVERT: H 38 TRP cc_start: 0.8957 (m100) cc_final: 0.8341 (m100) REVERT: H 82 LEU cc_start: 0.8698 (tp) cc_final: 0.8257 (tp) REVERT: H 83 GLN cc_start: 0.9372 (tp40) cc_final: 0.9036 (tp40) REVERT: I 34 THR cc_start: 0.9194 (m) cc_final: 0.8925 (m) REVERT: I 42 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8186 (tm-30) REVERT: I 57 LYS cc_start: 0.9478 (mmmm) cc_final: 0.9089 (mmmm) REVERT: I 85 GLU cc_start: 0.8983 (tt0) cc_final: 0.8647 (tm-30) REVERT: I 95 HIS cc_start: 0.8662 (t-90) cc_final: 0.8268 (t-170) REVERT: I 150 GLN cc_start: 0.9071 (mt0) cc_final: 0.8654 (mt0) REVERT: J 22 LEU cc_start: 0.9614 (mt) cc_final: 0.9353 (mt) REVERT: J 24 CYS cc_start: 0.9047 (t) cc_final: 0.8655 (t) REVERT: J 33 ARG cc_start: 0.9035 (ptm-80) cc_final: 0.8684 (ptm-80) REVERT: J 38 TRP cc_start: 0.8940 (m100) cc_final: 0.8195 (m100) REVERT: J 73 ARG cc_start: 0.7786 (ttm-80) cc_final: 0.7384 (ttm170) REVERT: J 82 LEU cc_start: 0.8787 (tp) cc_final: 0.8381 (tp) REVERT: J 83 GLN cc_start: 0.9391 (tp40) cc_final: 0.9132 (tp40) outliers start: 0 outliers final: 0 residues processed: 684 average time/residue: 0.2250 time to fit residues: 220.6971 Evaluate side-chains 638 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 638 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 31 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 129 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN A 59 GLN A 137 GLN ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 GLN ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.065463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.050792 restraints weight = 93856.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.054389 restraints weight = 35197.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.056875 restraints weight = 17537.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.058460 restraints weight = 10045.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.059476 restraints weight = 6345.799| |-----------------------------------------------------------------------------| r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 13090 Z= 0.283 Angle : 0.644 7.971 17770 Z= 0.353 Chirality : 0.044 0.156 1935 Planarity : 0.005 0.031 2265 Dihedral : 5.123 16.107 1770 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 56.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % 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: -3.70 (0.18), residues: 1605 helix: 1.72 (0.59), residues: 55 sheet: -2.98 (0.21), residues: 490 loop : -2.54 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 68 TYR 0.014 0.002 TYR E 54 PHE 0.017 0.002 PHE G 109 TRP 0.008 0.002 TRP E 205 HIS 0.007 0.002 HIS H 60 Details of bonding type rmsd covalent geometry : bond 0.00581 (13085) covalent geometry : angle 0.64342 (17760) SS BOND : bond 0.00740 ( 5) SS BOND : angle 1.47477 ( 10) hydrogen bonds : bond 0.04266 ( 405) hydrogen bonds : angle 7.99043 ( 885) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 659 time to evaluate : 0.642 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 THR cc_start: 0.9094 (m) cc_final: 0.8720 (m) REVERT: C 36 CYS cc_start: 0.7639 (m) cc_final: 0.7243 (m) REVERT: C 42 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8263 (tm-30) REVERT: C 62 GLU cc_start: 0.9149 (tp30) cc_final: 0.8591 (tp30) REVERT: C 68 SER cc_start: 0.9474 (m) cc_final: 0.9231 (p) REVERT: C 85 GLU cc_start: 0.9120 (tt0) cc_final: 0.8837 (tm-30) REVERT: C 95 HIS cc_start: 0.8539 (t-90) cc_final: 0.7832 (t-170) REVERT: C 116 ARG cc_start: 0.8152 (mmt-90) cc_final: 0.7575 (mmm-85) REVERT: C 145 ASN cc_start: 0.9110 (m110) cc_final: 0.8801 (m110) REVERT: C 183 ASN cc_start: 0.9410 (p0) cc_final: 0.9192 (p0) REVERT: D 20 LEU cc_start: 0.9360 (tp) cc_final: 0.9096 (tp) REVERT: D 22 LEU cc_start: 0.9631 (mt) cc_final: 0.9278 (mt) REVERT: D 33 ARG cc_start: 0.9070 (ptm-80) cc_final: 0.8786 (ptm-80) REVERT: D 35 THR cc_start: 0.9329 (m) cc_final: 0.8828 (m) REVERT: D 38 TRP cc_start: 0.8882 (m100) cc_final: 0.8026 (m100) REVERT: D 82 LEU cc_start: 0.8901 (tp) cc_final: 0.8540 (tp) REVERT: D 100 PHE cc_start: 0.8664 (p90) cc_final: 0.8187 (p90) REVERT: A 34 THR cc_start: 0.9157 (m) cc_final: 0.8827 (m) REVERT: A 42 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8328 (tm-30) REVERT: A 62 GLU cc_start: 0.9165 (tp30) cc_final: 0.8638 (tp30) REVERT: A 85 GLU cc_start: 0.9098 (tt0) cc_final: 0.8674 (tm-30) REVERT: A 95 HIS cc_start: 0.9088 (t-170) cc_final: 0.8460 (t70) REVERT: A 145 ASN cc_start: 0.9063 (m110) cc_final: 0.8783 (m110) REVERT: A 155 ASP cc_start: 0.8595 (p0) cc_final: 0.8334 (p0) REVERT: A 163 ASP cc_start: 0.9406 (p0) cc_final: 0.9184 (p0) REVERT: B 22 LEU cc_start: 0.9700 (mt) cc_final: 0.9346 (mt) REVERT: B 33 ARG cc_start: 0.9033 (ptm-80) cc_final: 0.8653 (ptm-80) REVERT: B 35 THR cc_start: 0.9420 (m) cc_final: 0.8914 (m) REVERT: B 38 TRP cc_start: 0.8983 (m100) cc_final: 0.8161 (m100) REVERT: B 48 ASP cc_start: 0.9134 (t70) cc_final: 0.8913 (t70) REVERT: B 82 LEU cc_start: 0.8992 (tp) cc_final: 0.8535 (tp) REVERT: B 100 PHE cc_start: 0.8750 (p90) cc_final: 0.8289 (p90) REVERT: E 34 THR cc_start: 0.9090 (m) cc_final: 0.8726 (m) REVERT: E 36 CYS cc_start: 0.7586 (m) cc_final: 0.7080 (m) REVERT: E 40 TYR cc_start: 0.9142 (t80) cc_final: 0.8896 (t80) REVERT: E 42 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8263 (tm-30) REVERT: E 85 GLU cc_start: 0.9095 (tt0) cc_final: 0.8782 (tm-30) REVERT: E 95 HIS cc_start: 0.8603 (t-90) cc_final: 0.7934 (t-170) REVERT: E 109 PHE cc_start: 0.9057 (t80) cc_final: 0.8316 (t80) REVERT: E 116 ARG cc_start: 0.8416 (mmt-90) cc_final: 0.8091 (mmm-85) REVERT: E 145 ASN cc_start: 0.9075 (m110) cc_final: 0.8798 (m110) REVERT: E 155 ASP cc_start: 0.8544 (p0) cc_final: 0.8223 (p0) REVERT: E 163 ASP cc_start: 0.9407 (p0) cc_final: 0.9196 (p0) REVERT: F 3 HIS cc_start: 0.9050 (m-70) cc_final: 0.8788 (p-80) REVERT: F 22 LEU cc_start: 0.9653 (mt) cc_final: 0.9233 (mt) REVERT: F 33 ARG cc_start: 0.9100 (ptm-80) cc_final: 0.8869 (ptm-80) REVERT: F 35 THR cc_start: 0.9403 (m) cc_final: 0.9161 (m) REVERT: F 38 TRP cc_start: 0.8819 (m100) cc_final: 0.8145 (m100) REVERT: F 54 THR cc_start: 0.8712 (p) cc_final: 0.8019 (p) REVERT: F 82 LEU cc_start: 0.8952 (tp) cc_final: 0.8387 (tp) REVERT: G 31 LYS cc_start: 0.9520 (mtpp) cc_final: 0.9300 (mtpp) REVERT: G 34 THR cc_start: 0.9146 (m) cc_final: 0.8793 (m) REVERT: G 36 CYS cc_start: 0.7458 (m) cc_final: 0.7179 (m) REVERT: G 42 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8288 (tm-30) REVERT: G 68 SER cc_start: 0.9521 (m) cc_final: 0.9244 (p) REVERT: G 85 GLU cc_start: 0.9038 (tt0) cc_final: 0.8708 (tm-30) REVERT: G 95 HIS cc_start: 0.9206 (t-170) cc_final: 0.8926 (t-170) REVERT: G 116 ARG cc_start: 0.8373 (mmt-90) cc_final: 0.8052 (mmm-85) REVERT: G 145 ASN cc_start: 0.9026 (m110) cc_final: 0.8760 (m110) REVERT: G 163 ASP cc_start: 0.9394 (p0) cc_final: 0.9152 (p0) REVERT: G 201 LYS cc_start: 0.9344 (mtmt) cc_final: 0.9099 (mtmm) REVERT: H 22 LEU cc_start: 0.9637 (mt) cc_final: 0.9168 (mt) REVERT: H 33 ARG cc_start: 0.9110 (ptm-80) cc_final: 0.8838 (ptm-80) REVERT: H 35 THR cc_start: 0.9369 (m) cc_final: 0.9168 (m) REVERT: H 38 TRP cc_start: 0.8730 (m100) cc_final: 0.8136 (m100) REVERT: H 82 LEU cc_start: 0.8912 (tp) cc_final: 0.8321 (tp) REVERT: I 34 THR cc_start: 0.9151 (m) cc_final: 0.8812 (m) REVERT: I 36 CYS cc_start: 0.7476 (m) cc_final: 0.6918 (m) REVERT: I 42 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8331 (tm-30) REVERT: I 62 GLU cc_start: 0.9147 (tp30) cc_final: 0.8627 (tp30) REVERT: I 85 GLU cc_start: 0.9083 (tt0) cc_final: 0.8653 (tm-30) REVERT: I 95 HIS cc_start: 0.8655 (t-90) cc_final: 0.7679 (t-170) REVERT: I 145 ASN cc_start: 0.9036 (m110) cc_final: 0.8727 (m110) REVERT: J 22 LEU cc_start: 0.9634 (mt) cc_final: 0.9252 (mt) REVERT: J 33 ARG cc_start: 0.9084 (ptm-80) cc_final: 0.8753 (ptm-80) REVERT: J 35 THR cc_start: 0.9347 (m) cc_final: 0.9095 (m) REVERT: J 38 TRP cc_start: 0.8875 (m100) cc_final: 0.8089 (m100) REVERT: J 54 THR cc_start: 0.8667 (p) cc_final: 0.7948 (p) REVERT: J 82 LEU cc_start: 0.8973 (tp) cc_final: 0.8426 (tp) outliers start: 0 outliers final: 0 residues processed: 659 average time/residue: 0.2231 time to fit residues: 211.8418 Evaluate side-chains 612 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 612 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 86 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 29 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 125 optimal weight: 0.6980 chunk 116 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 GLN ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 160 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 = 0.3019 r_free = 0.3019 target = 0.066726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.051662 restraints weight = 92287.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.055400 restraints weight = 34659.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.057887 restraints weight = 17226.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.059557 restraints weight = 9887.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.060632 restraints weight = 6247.796| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 13090 Z= 0.216 Angle : 0.582 5.921 17770 Z= 0.317 Chirality : 0.044 0.149 1935 Planarity : 0.004 0.032 2265 Dihedral : 4.973 16.397 1770 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 54.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % 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: -3.59 (0.18), residues: 1605 helix: 1.57 (0.61), residues: 55 sheet: -2.91 (0.21), residues: 490 loop : -2.44 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 118 TYR 0.013 0.001 TYR E 54 PHE 0.018 0.002 PHE C 11 TRP 0.009 0.001 TRP E 205 HIS 0.005 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00453 (13085) covalent geometry : angle 0.58064 (17760) SS BOND : bond 0.00548 ( 5) SS BOND : angle 1.47448 ( 10) hydrogen bonds : bond 0.03866 ( 405) hydrogen bonds : angle 7.73761 ( 885) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 681 time to evaluate : 0.623 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 31 LYS cc_start: 0.9498 (mtpp) cc_final: 0.9273 (mtpp) REVERT: C 34 THR cc_start: 0.9085 (m) cc_final: 0.8676 (m) REVERT: C 36 CYS cc_start: 0.7595 (m) cc_final: 0.7177 (m) REVERT: C 42 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8268 (tm-30) REVERT: C 62 GLU cc_start: 0.9118 (tp30) cc_final: 0.8449 (tp30) REVERT: C 85 GLU cc_start: 0.9112 (tt0) cc_final: 0.8669 (tm-30) REVERT: C 95 HIS cc_start: 0.8617 (t-90) cc_final: 0.7736 (t-170) REVERT: C 125 TYR cc_start: 0.7930 (t80) cc_final: 0.7704 (t80) REVERT: C 145 ASN cc_start: 0.9086 (m110) cc_final: 0.8752 (m110) REVERT: C 155 ASP cc_start: 0.8605 (p0) cc_final: 0.8324 (p0) REVERT: D 22 LEU cc_start: 0.9584 (mt) cc_final: 0.9239 (mt) REVERT: D 24 CYS cc_start: 0.8823 (t) cc_final: 0.8565 (t) REVERT: D 33 ARG cc_start: 0.9079 (ptm-80) cc_final: 0.8705 (ptm-80) REVERT: D 35 THR cc_start: 0.9294 (m) cc_final: 0.8835 (m) REVERT: D 38 TRP cc_start: 0.8808 (m100) cc_final: 0.7998 (m100) REVERT: D 48 ASP cc_start: 0.9264 (t70) cc_final: 0.9010 (t70) REVERT: D 82 LEU cc_start: 0.8500 (tp) cc_final: 0.8128 (tp) REVERT: D 100 PHE cc_start: 0.8650 (p90) cc_final: 0.8169 (p90) REVERT: D 105 ASP cc_start: 0.8946 (p0) cc_final: 0.8560 (p0) REVERT: D 110 TYR cc_start: 0.7800 (m-80) cc_final: 0.7551 (m-80) REVERT: A 34 THR cc_start: 0.9114 (m) cc_final: 0.8791 (m) REVERT: A 42 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8303 (tm-30) REVERT: A 62 GLU cc_start: 0.9113 (tp30) cc_final: 0.8602 (tp30) REVERT: A 85 GLU cc_start: 0.9086 (tt0) cc_final: 0.8686 (tm-30) REVERT: A 95 HIS cc_start: 0.9183 (t-170) cc_final: 0.8869 (t70) REVERT: A 145 ASN cc_start: 0.9051 (m110) cc_final: 0.8760 (m110) REVERT: A 155 ASP cc_start: 0.8534 (p0) cc_final: 0.8269 (p0) REVERT: B 22 LEU cc_start: 0.9624 (mt) cc_final: 0.9294 (mt) REVERT: B 24 CYS cc_start: 0.8733 (t) cc_final: 0.8431 (t) REVERT: B 33 ARG cc_start: 0.9061 (ptm-80) cc_final: 0.8696 (ptm-80) REVERT: B 35 THR cc_start: 0.9403 (m) cc_final: 0.8888 (m) REVERT: B 38 TRP cc_start: 0.8843 (m100) cc_final: 0.8028 (m100) REVERT: B 48 ASP cc_start: 0.9143 (t70) cc_final: 0.8937 (t70) REVERT: B 81 TYR cc_start: 0.8835 (m-80) cc_final: 0.8589 (m-80) REVERT: B 82 LEU cc_start: 0.8672 (tp) cc_final: 0.8348 (tp) REVERT: B 100 PHE cc_start: 0.8665 (p90) cc_final: 0.8191 (p90) REVERT: B 105 ASP cc_start: 0.8883 (p0) cc_final: 0.8586 (p0) REVERT: E 34 THR cc_start: 0.9029 (m) cc_final: 0.8672 (m) REVERT: E 36 CYS cc_start: 0.7622 (m) cc_final: 0.7232 (m) REVERT: E 40 TYR cc_start: 0.9116 (t80) cc_final: 0.8841 (t80) REVERT: E 42 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8262 (tm-30) REVERT: E 85 GLU cc_start: 0.9073 (tt0) cc_final: 0.8754 (tm-30) REVERT: E 95 HIS cc_start: 0.8651 (t-90) cc_final: 0.8220 (t-170) REVERT: E 109 PHE cc_start: 0.9080 (t80) cc_final: 0.8538 (t80) REVERT: E 116 ARG cc_start: 0.8344 (mmt-90) cc_final: 0.8095 (mmm-85) REVERT: E 145 ASN cc_start: 0.9090 (m110) cc_final: 0.8780 (m110) REVERT: E 155 ASP cc_start: 0.8463 (p0) cc_final: 0.8099 (p0) REVERT: E 163 ASP cc_start: 0.9360 (p0) cc_final: 0.9151 (p0) REVERT: F 22 LEU cc_start: 0.9579 (mt) cc_final: 0.9346 (mt) REVERT: F 24 CYS cc_start: 0.8581 (t) cc_final: 0.8168 (t) REVERT: F 33 ARG cc_start: 0.9126 (ptm-80) cc_final: 0.8811 (ptm-80) REVERT: F 38 TRP cc_start: 0.8701 (m100) cc_final: 0.7947 (m100) REVERT: F 82 LEU cc_start: 0.8706 (tp) cc_final: 0.8273 (tp) REVERT: F 105 ASP cc_start: 0.8930 (p0) cc_final: 0.8663 (p0) REVERT: G 14 GLU cc_start: 0.9169 (pm20) cc_final: 0.8941 (pm20) REVERT: G 31 LYS cc_start: 0.9512 (mtpp) cc_final: 0.9285 (mtpp) REVERT: G 34 THR cc_start: 0.9000 (m) cc_final: 0.8653 (m) REVERT: G 36 CYS cc_start: 0.7490 (m) cc_final: 0.7196 (m) REVERT: G 42 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8267 (tm-30) REVERT: G 62 GLU cc_start: 0.9133 (tp30) cc_final: 0.8757 (tp30) REVERT: G 85 GLU cc_start: 0.9045 (tt0) cc_final: 0.8722 (tm-30) REVERT: G 95 HIS cc_start: 0.9032 (t-170) cc_final: 0.8611 (t-170) REVERT: G 116 ARG cc_start: 0.8359 (mmt-90) cc_final: 0.8089 (mmm-85) REVERT: G 145 ASN cc_start: 0.9014 (m110) cc_final: 0.8727 (m110) REVERT: G 163 ASP cc_start: 0.9361 (p0) cc_final: 0.9141 (p0) REVERT: G 201 LYS cc_start: 0.9306 (mtmt) cc_final: 0.9064 (mtmm) REVERT: H 3 HIS cc_start: 0.9107 (m-70) cc_final: 0.8751 (p-80) REVERT: H 22 LEU cc_start: 0.9637 (mt) cc_final: 0.9140 (mt) REVERT: H 33 ARG cc_start: 0.9108 (ptm-80) cc_final: 0.8814 (ptm-80) REVERT: H 35 THR cc_start: 0.9364 (m) cc_final: 0.8656 (m) REVERT: H 38 TRP cc_start: 0.8569 (m100) cc_final: 0.8081 (m100) REVERT: H 82 LEU cc_start: 0.8864 (tp) cc_final: 0.8430 (tp) REVERT: H 100 PHE cc_start: 0.8565 (p90) cc_final: 0.8091 (p90) REVERT: H 110 TYR cc_start: 0.7854 (m-80) cc_final: 0.7653 (m-80) REVERT: I 34 THR cc_start: 0.9052 (m) cc_final: 0.8679 (m) REVERT: I 36 CYS cc_start: 0.7386 (m) cc_final: 0.7021 (m) REVERT: I 42 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8344 (tm-30) REVERT: I 62 GLU cc_start: 0.9137 (tp30) cc_final: 0.8635 (tp30) REVERT: I 85 GLU cc_start: 0.9091 (tt0) cc_final: 0.8684 (tm-30) REVERT: I 95 HIS cc_start: 0.8631 (t-90) cc_final: 0.7818 (t-170) REVERT: I 145 ASN cc_start: 0.9069 (m110) cc_final: 0.8753 (m110) REVERT: I 163 ASP cc_start: 0.9302 (p0) cc_final: 0.9100 (p0) REVERT: J 22 LEU cc_start: 0.9636 (mt) cc_final: 0.9303 (mt) REVERT: J 24 CYS cc_start: 0.8859 (t) cc_final: 0.8515 (t) REVERT: J 33 ARG cc_start: 0.9092 (ptm-80) cc_final: 0.8738 (ptm-80) REVERT: J 38 TRP cc_start: 0.8665 (m100) cc_final: 0.7945 (m100) REVERT: J 82 LEU cc_start: 0.8896 (tp) cc_final: 0.8440 (tp) outliers start: 0 outliers final: 0 residues processed: 681 average time/residue: 0.2194 time to fit residues: 215.0695 Evaluate side-chains 640 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 640 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 93 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 82 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 GLN ** I 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.064588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.049828 restraints weight = 94310.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.053416 restraints weight = 35701.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.055878 restraints weight = 17822.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.057398 restraints weight = 10210.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.058465 restraints weight = 6570.234| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 13090 Z= 0.276 Angle : 0.634 7.448 17770 Z= 0.342 Chirality : 0.044 0.154 1935 Planarity : 0.005 0.059 2265 Dihedral : 5.155 16.545 1770 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 58.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: -3.62 (0.18), residues: 1605 helix: 1.36 (0.58), residues: 55 sheet: -2.99 (0.21), residues: 490 loop : -2.42 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 47 TYR 0.014 0.002 TYR I 54 PHE 0.015 0.002 PHE E 109 TRP 0.016 0.002 TRP F 112 HIS 0.006 0.002 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00568 (13085) covalent geometry : angle 0.63362 (17760) SS BOND : bond 0.00689 ( 5) SS BOND : angle 1.35186 ( 10) hydrogen bonds : bond 0.04038 ( 405) hydrogen bonds : angle 7.78084 ( 885) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 679 time to evaluate : 0.573 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: C 31 LYS cc_start: 0.9530 (mtpp) cc_final: 0.9066 (mtpp) REVERT: C 34 THR cc_start: 0.9085 (m) cc_final: 0.8696 (m) REVERT: C 36 CYS cc_start: 0.7695 (m) cc_final: 0.7221 (m) REVERT: C 42 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8346 (tm-30) REVERT: C 68 SER cc_start: 0.9533 (m) cc_final: 0.9207 (p) REVERT: C 85 GLU cc_start: 0.9128 (tt0) cc_final: 0.8750 (tm-30) REVERT: C 95 HIS cc_start: 0.8537 (t-90) cc_final: 0.7822 (t-170) REVERT: C 116 ARG cc_start: 0.8321 (mmt-90) cc_final: 0.8069 (mmm-85) REVERT: C 119 LYS cc_start: 0.9485 (mtpp) cc_final: 0.8855 (mtmt) REVERT: C 145 ASN cc_start: 0.9061 (m110) cc_final: 0.8725 (m110) REVERT: C 155 ASP cc_start: 0.8562 (p0) cc_final: 0.8329 (p0) REVERT: C 160 ASN cc_start: 0.9265 (m110) cc_final: 0.9015 (m110) REVERT: C 163 ASP cc_start: 0.9364 (p0) cc_final: 0.9145 (p0) REVERT: C 201 LYS cc_start: 0.9332 (mtmt) cc_final: 0.9049 (mtmm) REVERT: D 20 LEU cc_start: 0.9371 (tp) cc_final: 0.9161 (tp) REVERT: D 22 LEU cc_start: 0.9609 (mt) cc_final: 0.9145 (mt) REVERT: D 24 CYS cc_start: 0.8958 (t) cc_final: 0.8194 (t) REVERT: D 33 ARG cc_start: 0.9085 (ptm-80) cc_final: 0.8685 (ptm-80) REVERT: D 38 TRP cc_start: 0.8799 (m100) cc_final: 0.8060 (m100) REVERT: D 48 ASP cc_start: 0.9257 (t70) cc_final: 0.9021 (t70) REVERT: D 68 ARG cc_start: 0.7964 (mtp-110) cc_final: 0.7398 (mtp-110) REVERT: D 82 LEU cc_start: 0.8770 (tp) cc_final: 0.8396 (tp) REVERT: D 83 GLN cc_start: 0.9225 (tp40) cc_final: 0.9024 (tp40) REVERT: D 105 ASP cc_start: 0.8937 (p0) cc_final: 0.8556 (p0) REVERT: D 110 TYR cc_start: 0.7630 (m-80) cc_final: 0.7311 (m-80) REVERT: A 31 LYS cc_start: 0.9539 (mtpp) cc_final: 0.9072 (mmmm) REVERT: A 34 THR cc_start: 0.9076 (m) cc_final: 0.8747 (m) REVERT: A 36 CYS cc_start: 0.7516 (m) cc_final: 0.7308 (m) REVERT: A 42 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8343 (tm-30) REVERT: A 62 GLU cc_start: 0.9120 (tp30) cc_final: 0.8900 (tp30) REVERT: A 85 GLU cc_start: 0.9092 (tt0) cc_final: 0.8805 (tm-30) REVERT: A 95 HIS cc_start: 0.9197 (t-170) cc_final: 0.8459 (t70) REVERT: A 116 ARG cc_start: 0.8468 (mmt-90) cc_final: 0.8174 (mmm-85) REVERT: A 145 ASN cc_start: 0.9075 (m110) cc_final: 0.8796 (m110) REVERT: A 155 ASP cc_start: 0.8449 (p0) cc_final: 0.8115 (p0) REVERT: A 163 ASP cc_start: 0.9372 (p0) cc_final: 0.9115 (p0) REVERT: B 22 LEU cc_start: 0.9631 (mt) cc_final: 0.9172 (mt) REVERT: B 24 CYS cc_start: 0.8885 (t) cc_final: 0.8256 (t) REVERT: B 33 ARG cc_start: 0.9029 (ptm-80) cc_final: 0.8603 (ptm-80) REVERT: B 35 THR cc_start: 0.9390 (m) cc_final: 0.8830 (m) REVERT: B 38 TRP cc_start: 0.8849 (m100) cc_final: 0.8132 (m100) REVERT: B 82 LEU cc_start: 0.8731 (tp) cc_final: 0.8340 (tp) REVERT: B 100 PHE cc_start: 0.8737 (p90) cc_final: 0.8066 (p90) REVERT: B 105 ASP cc_start: 0.8898 (p0) cc_final: 0.8526 (p0) REVERT: B 110 TYR cc_start: 0.7728 (m-80) cc_final: 0.7501 (m-80) REVERT: E 31 LYS cc_start: 0.9531 (mtpp) cc_final: 0.9068 (mmmm) REVERT: E 34 THR cc_start: 0.9018 (m) cc_final: 0.8636 (m) REVERT: E 36 CYS cc_start: 0.7582 (m) cc_final: 0.7197 (m) REVERT: E 40 TYR cc_start: 0.9188 (t80) cc_final: 0.8907 (t80) REVERT: E 42 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8387 (tm-30) REVERT: E 85 GLU cc_start: 0.9085 (tt0) cc_final: 0.8723 (tm-30) REVERT: E 95 HIS cc_start: 0.8655 (t-90) cc_final: 0.7806 (t70) REVERT: E 116 ARG cc_start: 0.8494 (mmt-90) cc_final: 0.8134 (mmm-85) REVERT: E 145 ASN cc_start: 0.9086 (m110) cc_final: 0.8782 (m110) REVERT: E 155 ASP cc_start: 0.8479 (p0) cc_final: 0.8086 (p0) REVERT: E 163 ASP cc_start: 0.9337 (p0) cc_final: 0.9133 (p0) REVERT: F 7 VAL cc_start: 0.9353 (t) cc_final: 0.9142 (t) REVERT: F 22 LEU cc_start: 0.9620 (mt) cc_final: 0.9319 (mt) REVERT: F 24 CYS cc_start: 0.8698 (t) cc_final: 0.8104 (t) REVERT: F 33 ARG cc_start: 0.9130 (ptm-80) cc_final: 0.8876 (ptm-80) REVERT: F 34 TYR cc_start: 0.7675 (m-10) cc_final: 0.7229 (m-10) REVERT: F 35 THR cc_start: 0.9354 (m) cc_final: 0.9142 (m) REVERT: F 38 TRP cc_start: 0.8734 (m100) cc_final: 0.7999 (m100) REVERT: F 82 LEU cc_start: 0.8915 (tp) cc_final: 0.8367 (tp) REVERT: F 105 ASP cc_start: 0.8939 (p0) cc_final: 0.8587 (p0) REVERT: F 110 TYR cc_start: 0.7576 (m-80) cc_final: 0.7236 (m-80) REVERT: G 14 GLU cc_start: 0.9148 (pm20) cc_final: 0.8891 (pm20) REVERT: G 31 LYS cc_start: 0.9542 (mtpp) cc_final: 0.9318 (mtpp) REVERT: G 34 THR cc_start: 0.8992 (m) cc_final: 0.8621 (m) REVERT: G 36 CYS cc_start: 0.7462 (m) cc_final: 0.7101 (m) REVERT: G 42 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8320 (tm-30) REVERT: G 62 GLU cc_start: 0.9109 (tp30) cc_final: 0.8533 (tp30) REVERT: G 85 GLU cc_start: 0.9042 (tt0) cc_final: 0.8712 (tm-30) REVERT: G 95 HIS cc_start: 0.8880 (t-170) cc_final: 0.8470 (t-170) REVERT: G 116 ARG cc_start: 0.8491 (mmt-90) cc_final: 0.8153 (mmm-85) REVERT: G 119 LYS cc_start: 0.9397 (mtpt) cc_final: 0.8960 (mtmt) REVERT: G 163 ASP cc_start: 0.9333 (p0) cc_final: 0.9098 (p0) REVERT: G 201 LYS cc_start: 0.9291 (mtmt) cc_final: 0.9040 (mtmm) REVERT: H 22 LEU cc_start: 0.9556 (mt) cc_final: 0.9155 (mt) REVERT: H 33 ARG cc_start: 0.9111 (ptm-80) cc_final: 0.8770 (ptm-80) REVERT: H 35 THR cc_start: 0.9322 (m) cc_final: 0.8687 (m) REVERT: H 38 TRP cc_start: 0.8614 (m100) cc_final: 0.8144 (m100) REVERT: H 82 LEU cc_start: 0.8635 (tp) cc_final: 0.8055 (tp) REVERT: H 100 PHE cc_start: 0.8595 (p90) cc_final: 0.7920 (p90) REVERT: H 101 ARG cc_start: 0.8434 (ptt180) cc_final: 0.7424 (ptt180) REVERT: I 31 LYS cc_start: 0.9502 (mtpp) cc_final: 0.9005 (mmmm) REVERT: I 34 THR cc_start: 0.9054 (m) cc_final: 0.8692 (m) REVERT: I 36 CYS cc_start: 0.7426 (m) cc_final: 0.7027 (m) REVERT: I 42 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8400 (tm-30) REVERT: I 62 GLU cc_start: 0.9096 (tp30) cc_final: 0.8879 (tp30) REVERT: I 85 GLU cc_start: 0.9045 (tt0) cc_final: 0.8639 (tm-30) REVERT: I 95 HIS cc_start: 0.8617 (t-90) cc_final: 0.7714 (t-170) REVERT: I 109 PHE cc_start: 0.9463 (t80) cc_final: 0.9227 (t80) REVERT: I 145 ASN cc_start: 0.9025 (m110) cc_final: 0.8687 (m110) REVERT: I 163 ASP cc_start: 0.9302 (p0) cc_final: 0.9099 (p0) REVERT: J 22 LEU cc_start: 0.9589 (mt) cc_final: 0.9236 (mt) REVERT: J 33 ARG cc_start: 0.9082 (ptm-80) cc_final: 0.8637 (ptm-80) REVERT: J 35 THR cc_start: 0.9270 (m) cc_final: 0.9062 (m) REVERT: J 38 TRP cc_start: 0.8692 (m100) cc_final: 0.7745 (m-10) REVERT: J 71 ILE cc_start: 0.9378 (tp) cc_final: 0.8297 (tp) REVERT: J 82 LEU cc_start: 0.8636 (tp) cc_final: 0.8386 (tp) outliers start: 0 outliers final: 0 residues processed: 679 average time/residue: 0.2239 time to fit residues: 215.6743 Evaluate side-chains 612 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 612 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 86 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 GLN ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.063751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.048923 restraints weight = 93992.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.052488 restraints weight = 35701.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.054950 restraints weight = 17900.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.056508 restraints weight = 10280.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.057537 restraints weight = 6594.389| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 13090 Z= 0.283 Angle : 0.633 7.653 17770 Z= 0.340 Chirality : 0.044 0.140 1935 Planarity : 0.005 0.065 2265 Dihedral : 5.270 17.339 1770 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 62.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % 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: -3.80 (0.18), residues: 1605 helix: -0.81 (0.50), residues: 85 sheet: -2.90 (0.20), residues: 515 loop : -2.54 (0.16), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 47 TYR 0.013 0.002 TYR C 192 PHE 0.020 0.002 PHE C 11 TRP 0.019 0.002 TRP F 112 HIS 0.005 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00580 (13085) covalent geometry : angle 0.63204 (17760) SS BOND : bond 0.00697 ( 5) SS BOND : angle 1.21867 ( 10) hydrogen bonds : bond 0.03960 ( 405) hydrogen bonds : angle 7.79261 ( 885) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 681 time to evaluate : 0.612 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: C 31 LYS cc_start: 0.9539 (mtpp) cc_final: 0.9069 (mtpp) REVERT: C 34 THR cc_start: 0.9020 (m) cc_final: 0.8639 (m) REVERT: C 36 CYS cc_start: 0.7647 (m) cc_final: 0.6909 (m) REVERT: C 42 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8373 (tm-30) REVERT: C 81 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8178 (tm-30) REVERT: C 85 GLU cc_start: 0.9117 (tt0) cc_final: 0.8731 (tm-30) REVERT: C 95 HIS cc_start: 0.8701 (t-90) cc_final: 0.7527 (t70) REVERT: C 145 ASN cc_start: 0.9099 (m110) cc_final: 0.8774 (m110) REVERT: C 155 ASP cc_start: 0.8515 (p0) cc_final: 0.8295 (p0) REVERT: C 163 ASP cc_start: 0.9337 (p0) cc_final: 0.9134 (p0) REVERT: C 201 LYS cc_start: 0.9324 (mtmt) cc_final: 0.9023 (mtmm) REVERT: D 22 LEU cc_start: 0.9559 (mt) cc_final: 0.9150 (mt) REVERT: D 24 CYS cc_start: 0.8496 (t) cc_final: 0.8138 (t) REVERT: D 33 ARG cc_start: 0.9088 (ptm-80) cc_final: 0.8661 (ptm-80) REVERT: D 35 THR cc_start: 0.9289 (m) cc_final: 0.8982 (m) REVERT: D 38 TRP cc_start: 0.8753 (m100) cc_final: 0.8045 (m100) REVERT: D 48 ASP cc_start: 0.9250 (t70) cc_final: 0.9023 (t0) REVERT: D 54 THR cc_start: 0.8730 (p) cc_final: 0.8321 (p) REVERT: D 82 LEU cc_start: 0.8557 (tp) cc_final: 0.8122 (tp) REVERT: D 105 ASP cc_start: 0.8976 (p0) cc_final: 0.8626 (p0) REVERT: D 110 TYR cc_start: 0.7438 (m-80) cc_final: 0.7169 (m-80) REVERT: A 34 THR cc_start: 0.9031 (m) cc_final: 0.8697 (m) REVERT: A 36 CYS cc_start: 0.7557 (m) cc_final: 0.7147 (m) REVERT: A 42 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8365 (tm-30) REVERT: A 85 GLU cc_start: 0.9092 (tt0) cc_final: 0.8746 (tm-30) REVERT: A 145 ASN cc_start: 0.9097 (m110) cc_final: 0.8793 (m110) REVERT: A 155 ASP cc_start: 0.8393 (p0) cc_final: 0.8035 (p0) REVERT: A 163 ASP cc_start: 0.9350 (p0) cc_final: 0.9106 (p0) REVERT: B 22 LEU cc_start: 0.9630 (mt) cc_final: 0.9114 (mt) REVERT: B 33 ARG cc_start: 0.9032 (ptm-80) cc_final: 0.8598 (ptm-80) REVERT: B 35 THR cc_start: 0.9365 (m) cc_final: 0.8777 (m) REVERT: B 38 TRP cc_start: 0.8759 (m100) cc_final: 0.8262 (m100) REVERT: B 54 THR cc_start: 0.8717 (p) cc_final: 0.8313 (p) REVERT: B 81 TYR cc_start: 0.8843 (m-80) cc_final: 0.8617 (m-80) REVERT: B 82 LEU cc_start: 0.8837 (tp) cc_final: 0.8425 (tp) REVERT: B 100 PHE cc_start: 0.8594 (p90) cc_final: 0.7838 (p90) REVERT: B 105 ASP cc_start: 0.8891 (p0) cc_final: 0.8519 (p0) REVERT: B 110 TYR cc_start: 0.7450 (m-80) cc_final: 0.7217 (m-80) REVERT: E 34 THR cc_start: 0.8982 (m) cc_final: 0.8598 (m) REVERT: E 36 CYS cc_start: 0.7523 (m) cc_final: 0.7131 (m) REVERT: E 40 TYR cc_start: 0.9220 (t80) cc_final: 0.8891 (t80) REVERT: E 42 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8411 (tm-30) REVERT: E 85 GLU cc_start: 0.9076 (tt0) cc_final: 0.8696 (tm-30) REVERT: E 95 HIS cc_start: 0.8625 (t-90) cc_final: 0.8117 (t-170) REVERT: E 116 ARG cc_start: 0.8602 (mmt-90) cc_final: 0.8192 (mmm-85) REVERT: E 145 ASN cc_start: 0.9101 (m110) cc_final: 0.8798 (m110) REVERT: E 155 ASP cc_start: 0.8467 (p0) cc_final: 0.8061 (p0) REVERT: F 7 VAL cc_start: 0.9395 (t) cc_final: 0.9177 (t) REVERT: F 22 LEU cc_start: 0.9652 (mt) cc_final: 0.9208 (mt) REVERT: F 24 CYS cc_start: 0.8875 (t) cc_final: 0.7947 (t) REVERT: F 33 ARG cc_start: 0.9097 (ptm-80) cc_final: 0.8720 (ptm-80) REVERT: F 35 THR cc_start: 0.9334 (m) cc_final: 0.8996 (m) REVERT: F 38 TRP cc_start: 0.8636 (m100) cc_final: 0.8016 (m100) REVERT: F 54 THR cc_start: 0.7990 (p) cc_final: 0.7576 (p) REVERT: F 82 LEU cc_start: 0.9023 (tp) cc_final: 0.8466 (tp) REVERT: F 105 ASP cc_start: 0.8969 (p0) cc_final: 0.8644 (p0) REVERT: G 14 GLU cc_start: 0.9139 (pm20) cc_final: 0.8863 (pm20) REVERT: G 31 LYS cc_start: 0.9548 (mtpp) cc_final: 0.9091 (mtpp) REVERT: G 34 THR cc_start: 0.8977 (m) cc_final: 0.8624 (m) REVERT: G 36 CYS cc_start: 0.7449 (m) cc_final: 0.7178 (m) REVERT: G 42 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8366 (tm-30) REVERT: G 62 GLU cc_start: 0.9146 (tp30) cc_final: 0.8798 (tp30) REVERT: G 85 GLU cc_start: 0.9026 (tt0) cc_final: 0.8700 (tm-30) REVERT: G 95 HIS cc_start: 0.8925 (t-170) cc_final: 0.8445 (t-170) REVERT: G 116 ARG cc_start: 0.8554 (mmt-90) cc_final: 0.8180 (mmm-85) REVERT: G 145 ASN cc_start: 0.9045 (m110) cc_final: 0.8736 (m110) REVERT: G 163 ASP cc_start: 0.9333 (p0) cc_final: 0.9102 (p0) REVERT: G 201 LYS cc_start: 0.9287 (mtmt) cc_final: 0.9028 (mtmm) REVERT: H 22 LEU cc_start: 0.9597 (mt) cc_final: 0.9086 (mt) REVERT: H 33 ARG cc_start: 0.9087 (ptm-80) cc_final: 0.8737 (ptm-80) REVERT: H 35 THR cc_start: 0.9334 (m) cc_final: 0.8680 (m) REVERT: H 38 TRP cc_start: 0.8528 (m100) cc_final: 0.8129 (m100) REVERT: H 54 THR cc_start: 0.8594 (p) cc_final: 0.8230 (p) REVERT: H 82 LEU cc_start: 0.8887 (tp) cc_final: 0.8296 (tp) REVERT: H 100 PHE cc_start: 0.8582 (p90) cc_final: 0.7837 (p90) REVERT: H 101 ARG cc_start: 0.8350 (ptt180) cc_final: 0.7228 (ptt180) REVERT: H 105 ASP cc_start: 0.8857 (p0) cc_final: 0.8514 (p0) REVERT: H 110 TYR cc_start: 0.7548 (m-80) cc_final: 0.7343 (m-80) REVERT: I 34 THR cc_start: 0.9009 (m) cc_final: 0.8641 (m) REVERT: I 36 CYS cc_start: 0.7390 (m) cc_final: 0.7041 (m) REVERT: I 42 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8409 (tm-30) REVERT: I 62 GLU cc_start: 0.9058 (tp30) cc_final: 0.8857 (tp30) REVERT: I 85 GLU cc_start: 0.8991 (tt0) cc_final: 0.8671 (tm-30) REVERT: I 95 HIS cc_start: 0.8673 (t-90) cc_final: 0.7913 (t-170) REVERT: I 145 ASN cc_start: 0.9044 (m110) cc_final: 0.8716 (m110) REVERT: J 22 LEU cc_start: 0.9625 (mt) cc_final: 0.9116 (mt) REVERT: J 24 CYS cc_start: 0.9114 (t) cc_final: 0.8881 (t) REVERT: J 33 ARG cc_start: 0.9075 (ptm-80) cc_final: 0.8630 (ptm-80) REVERT: J 35 THR cc_start: 0.9272 (m) cc_final: 0.9049 (m) REVERT: J 38 TRP cc_start: 0.8774 (m100) cc_final: 0.7635 (m-10) REVERT: J 71 ILE cc_start: 0.9351 (tp) cc_final: 0.8226 (tp) REVERT: J 82 LEU cc_start: 0.8888 (tp) cc_final: 0.8440 (tp) outliers start: 0 outliers final: 0 residues processed: 681 average time/residue: 0.2307 time to fit residues: 222.4592 Evaluate side-chains 613 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 613 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 74 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.063185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.048146 restraints weight = 94539.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.051683 restraints weight = 36475.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.054131 restraints weight = 18476.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.055710 restraints weight = 10710.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.056773 restraints weight = 6852.211| |-----------------------------------------------------------------------------| r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 13090 Z= 0.307 Angle : 0.663 8.515 17770 Z= 0.355 Chirality : 0.045 0.158 1935 Planarity : 0.005 0.058 2265 Dihedral : 5.403 17.956 1770 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 65.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.79 (0.18), residues: 1605 helix: 0.90 (0.58), residues: 55 sheet: -2.98 (0.20), residues: 530 loop : -2.54 (0.16), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG H 47 TYR 0.023 0.002 TYR I 19 PHE 0.017 0.002 PHE F 69 TRP 0.020 0.002 TRP F 112 HIS 0.022 0.002 HIS I 38 Details of bonding type rmsd covalent geometry : bond 0.00631 (13085) covalent geometry : angle 0.66273 (17760) SS BOND : bond 0.00768 ( 5) SS BOND : angle 1.34142 ( 10) hydrogen bonds : bond 0.04072 ( 405) hydrogen bonds : angle 7.81823 ( 885) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 669 time to evaluate : 0.684 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash REVERT: C 7 LYS cc_start: 0.9010 (mtmm) cc_final: 0.8728 (mtmm) REVERT: C 31 LYS cc_start: 0.9543 (mtpp) cc_final: 0.9082 (mtpp) REVERT: C 36 CYS cc_start: 0.7457 (m) cc_final: 0.6973 (m) REVERT: C 42 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8439 (tm-30) REVERT: C 49 TYR cc_start: 0.9354 (p90) cc_final: 0.8973 (p90) REVERT: C 54 TYR cc_start: 0.9316 (t80) cc_final: 0.9055 (t80) REVERT: C 85 GLU cc_start: 0.9172 (tt0) cc_final: 0.8742 (tm-30) REVERT: C 95 HIS cc_start: 0.8678 (t-90) cc_final: 0.7528 (t-170) REVERT: C 119 LYS cc_start: 0.9465 (mtpp) cc_final: 0.8841 (mtmt) REVERT: C 145 ASN cc_start: 0.9104 (m110) cc_final: 0.8784 (m110) REVERT: C 201 LYS cc_start: 0.9307 (mtmt) cc_final: 0.8992 (mtmm) REVERT: D 22 LEU cc_start: 0.9598 (mt) cc_final: 0.9121 (mt) REVERT: D 33 ARG cc_start: 0.9115 (ptm-80) cc_final: 0.8706 (ptm160) REVERT: D 35 THR cc_start: 0.9252 (m) cc_final: 0.8822 (m) REVERT: D 38 TRP cc_start: 0.8767 (m100) cc_final: 0.7677 (m-10) REVERT: D 48 ASP cc_start: 0.9275 (t70) cc_final: 0.9045 (t0) REVERT: D 54 THR cc_start: 0.8700 (p) cc_final: 0.7072 (p) REVERT: D 68 ARG cc_start: 0.7970 (mtp-110) cc_final: 0.7139 (mtp-110) REVERT: D 71 ILE cc_start: 0.9307 (tp) cc_final: 0.7963 (tp) REVERT: D 101 ARG cc_start: 0.8460 (ptt90) cc_final: 0.7970 (ptt180) REVERT: D 105 ASP cc_start: 0.8901 (p0) cc_final: 0.8536 (p0) REVERT: D 110 TYR cc_start: 0.7790 (m-80) cc_final: 0.7440 (m-80) REVERT: A 42 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8422 (tm-30) REVERT: A 85 GLU cc_start: 0.9159 (tt0) cc_final: 0.8826 (tm-30) REVERT: A 145 ASN cc_start: 0.9088 (m110) cc_final: 0.8775 (m110) REVERT: A 155 ASP cc_start: 0.8334 (p0) cc_final: 0.7986 (p0) REVERT: B 22 LEU cc_start: 0.9649 (mt) cc_final: 0.9097 (mt) REVERT: B 33 ARG cc_start: 0.9120 (ptm-80) cc_final: 0.8724 (ptm160) REVERT: B 35 THR cc_start: 0.9312 (m) cc_final: 0.8897 (m) REVERT: B 38 TRP cc_start: 0.8762 (m100) cc_final: 0.7799 (m-10) REVERT: B 71 ILE cc_start: 0.9374 (tp) cc_final: 0.8585 (tp) REVERT: B 82 LEU cc_start: 0.8890 (tp) cc_final: 0.8481 (tp) REVERT: B 100 PHE cc_start: 0.8780 (p90) cc_final: 0.7965 (p90) REVERT: B 105 ASP cc_start: 0.8891 (p0) cc_final: 0.8512 (p0) REVERT: B 110 TYR cc_start: 0.7664 (m-80) cc_final: 0.7374 (m-80) REVERT: E 31 LYS cc_start: 0.9547 (mtpp) cc_final: 0.9168 (mmmt) REVERT: E 34 THR cc_start: 0.8928 (m) cc_final: 0.8577 (m) REVERT: E 37 LEU cc_start: 0.9588 (pp) cc_final: 0.9363 (pp) REVERT: E 40 TYR cc_start: 0.9269 (t80) cc_final: 0.8983 (t80) REVERT: E 42 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8464 (tm-30) REVERT: E 85 GLU cc_start: 0.9085 (tt0) cc_final: 0.8717 (tm-30) REVERT: E 95 HIS cc_start: 0.8691 (t-90) cc_final: 0.8198 (t70) REVERT: E 116 ARG cc_start: 0.8647 (mmt-90) cc_final: 0.8226 (mmm-85) REVERT: E 145 ASN cc_start: 0.9088 (m110) cc_final: 0.8800 (m110) REVERT: E 155 ASP cc_start: 0.8469 (p0) cc_final: 0.8074 (p0) REVERT: F 33 ARG cc_start: 0.9110 (ptm-80) cc_final: 0.8725 (ptm-80) REVERT: F 35 THR cc_start: 0.9293 (m) cc_final: 0.9085 (m) REVERT: F 82 LEU cc_start: 0.8870 (tp) cc_final: 0.8311 (tp) REVERT: F 105 ASP cc_start: 0.8963 (p0) cc_final: 0.8622 (p0) REVERT: G 14 GLU cc_start: 0.9129 (pm20) cc_final: 0.8866 (pm20) REVERT: G 31 LYS cc_start: 0.9546 (mtpp) cc_final: 0.9089 (mtpp) REVERT: G 34 THR cc_start: 0.8978 (m) cc_final: 0.8606 (m) REVERT: G 36 CYS cc_start: 0.7405 (m) cc_final: 0.7039 (m) REVERT: G 42 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8441 (tm-30) REVERT: G 62 GLU cc_start: 0.9130 (tp30) cc_final: 0.8851 (tp30) REVERT: G 85 GLU cc_start: 0.9025 (tt0) cc_final: 0.8671 (tm-30) REVERT: G 95 HIS cc_start: 0.8871 (t-170) cc_final: 0.8493 (t-170) REVERT: G 145 ASN cc_start: 0.9060 (m110) cc_final: 0.8758 (m110) REVERT: G 163 ASP cc_start: 0.9328 (p0) cc_final: 0.9091 (p0) REVERT: G 201 LYS cc_start: 0.9266 (mtmt) cc_final: 0.9033 (mtmm) REVERT: H 8 GLU cc_start: 0.8638 (pm20) cc_final: 0.8115 (pm20) REVERT: H 22 LEU cc_start: 0.9641 (mt) cc_final: 0.9336 (mt) REVERT: H 33 ARG cc_start: 0.9083 (ptm-80) cc_final: 0.8688 (ptm-80) REVERT: H 35 THR cc_start: 0.9285 (m) cc_final: 0.8766 (m) REVERT: H 53 ILE cc_start: 0.9532 (tt) cc_final: 0.9192 (tt) REVERT: H 68 ARG cc_start: 0.7714 (mtp-110) cc_final: 0.7132 (mtp-110) REVERT: H 82 LEU cc_start: 0.8937 (tp) cc_final: 0.8345 (tp) REVERT: H 100 PHE cc_start: 0.8524 (p90) cc_final: 0.7823 (p90) REVERT: H 105 ASP cc_start: 0.8908 (p0) cc_final: 0.8469 (p0) REVERT: I 36 CYS cc_start: 0.7358 (m) cc_final: 0.6898 (m) REVERT: I 42 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8453 (tm-30) REVERT: I 85 GLU cc_start: 0.9013 (tt0) cc_final: 0.8757 (tm-30) REVERT: I 95 HIS cc_start: 0.8710 (t-90) cc_final: 0.8187 (t-90) REVERT: I 145 ASN cc_start: 0.9095 (m110) cc_final: 0.8784 (m110) REVERT: I 197 GLU cc_start: 0.8817 (tp30) cc_final: 0.8515 (tp30) REVERT: J 8 GLU cc_start: 0.8638 (pm20) cc_final: 0.8032 (pm20) REVERT: J 22 LEU cc_start: 0.9668 (mt) cc_final: 0.9082 (mt) REVERT: J 33 ARG cc_start: 0.9113 (ptm-80) cc_final: 0.8684 (ptm-80) REVERT: J 35 THR cc_start: 0.9246 (m) cc_final: 0.9016 (m) REVERT: J 38 TRP cc_start: 0.8807 (m100) cc_final: 0.7580 (m-10) REVERT: J 71 ILE cc_start: 0.9331 (tp) cc_final: 0.8075 (tp) REVERT: J 82 LEU cc_start: 0.8943 (tp) cc_final: 0.8381 (tp) outliers start: 0 outliers final: 0 residues processed: 669 average time/residue: 0.2294 time to fit residues: 217.9787 Evaluate side-chains 609 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 609 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 7 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 83 optimal weight: 20.0000 chunk 106 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 160 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 = 0.3014 r_free = 0.3014 target = 0.067138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.051576 restraints weight = 90168.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.055346 restraints weight = 34815.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.057969 restraints weight = 17501.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.059631 restraints weight = 10103.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.060782 restraints weight = 6487.148| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13090 Z= 0.149 Angle : 0.566 5.024 17770 Z= 0.308 Chirality : 0.044 0.152 1935 Planarity : 0.004 0.047 2265 Dihedral : 5.133 18.177 1770 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 50.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.50 (0.18), residues: 1605 helix: 1.23 (0.65), residues: 55 sheet: -2.82 (0.20), residues: 530 loop : -2.31 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 47 TYR 0.022 0.001 TYR I 19 PHE 0.017 0.002 PHE F 69 TRP 0.016 0.002 TRP F 112 HIS 0.015 0.001 HIS I 38 Details of bonding type rmsd covalent geometry : bond 0.00334 (13085) covalent geometry : angle 0.56463 (17760) SS BOND : bond 0.00341 ( 5) SS BOND : angle 1.50071 ( 10) hydrogen bonds : bond 0.03357 ( 405) hydrogen bonds : angle 7.41574 ( 885) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 686 time to evaluate : 0.589 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash REVERT: C 31 LYS cc_start: 0.9510 (mtpp) cc_final: 0.8985 (mmmm) REVERT: C 34 THR cc_start: 0.8939 (m) cc_final: 0.8591 (m) REVERT: C 36 CYS cc_start: 0.7523 (m) cc_final: 0.7002 (m) REVERT: C 42 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8337 (tm-30) REVERT: C 54 TYR cc_start: 0.9294 (t80) cc_final: 0.9080 (t80) REVERT: C 66 PHE cc_start: 0.8844 (t80) cc_final: 0.8550 (t80) REVERT: C 85 GLU cc_start: 0.9159 (tt0) cc_final: 0.8719 (tm-30) REVERT: C 95 HIS cc_start: 0.8721 (t-90) cc_final: 0.7875 (t-170) REVERT: C 145 ASN cc_start: 0.9091 (m110) cc_final: 0.8769 (m110) REVERT: C 155 ASP cc_start: 0.8436 (p0) cc_final: 0.8146 (p0) REVERT: D 20 LEU cc_start: 0.9418 (tp) cc_final: 0.9160 (tp) REVERT: D 22 LEU cc_start: 0.9626 (mt) cc_final: 0.9147 (mt) REVERT: D 24 CYS cc_start: 0.8802 (t) cc_final: 0.8459 (t) REVERT: D 33 ARG cc_start: 0.9141 (ptm-80) cc_final: 0.8725 (ptm-80) REVERT: D 38 TRP cc_start: 0.8599 (m100) cc_final: 0.8002 (m100) REVERT: D 48 ASP cc_start: 0.9203 (t70) cc_final: 0.8907 (t70) REVERT: D 68 ARG cc_start: 0.7997 (mtp-110) cc_final: 0.7196 (mtp-110) REVERT: D 82 LEU cc_start: 0.8806 (tp) cc_final: 0.8407 (tp) REVERT: D 83 GLN cc_start: 0.9154 (tp40) cc_final: 0.8902 (tp-100) REVERT: D 101 ARG cc_start: 0.8260 (ptt90) cc_final: 0.7406 (ptt180) REVERT: D 105 ASP cc_start: 0.8889 (p0) cc_final: 0.8550 (p0) REVERT: D 110 TYR cc_start: 0.7822 (m-80) cc_final: 0.7474 (m-80) REVERT: A 31 LYS cc_start: 0.9525 (mtpp) cc_final: 0.9011 (mmmm) REVERT: A 42 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8321 (tm-30) REVERT: A 85 GLU cc_start: 0.9124 (tt0) cc_final: 0.8729 (tm-30) REVERT: A 95 HIS cc_start: 0.9292 (t-170) cc_final: 0.9089 (t70) REVERT: A 112 ASP cc_start: 0.8940 (t0) cc_final: 0.8739 (t0) REVERT: A 145 ASN cc_start: 0.9151 (m110) cc_final: 0.8828 (m110) REVERT: A 155 ASP cc_start: 0.8238 (p0) cc_final: 0.7855 (p0) REVERT: B 19 SER cc_start: 0.9433 (p) cc_final: 0.9193 (m) REVERT: B 22 LEU cc_start: 0.9677 (mt) cc_final: 0.9141 (mt) REVERT: B 33 ARG cc_start: 0.9080 (ptm-80) cc_final: 0.8670 (ptm-80) REVERT: B 35 THR cc_start: 0.9298 (m) cc_final: 0.8835 (m) REVERT: B 38 TRP cc_start: 0.8570 (m100) cc_final: 0.8185 (m100) REVERT: B 64 SER cc_start: 0.9481 (p) cc_final: 0.9149 (p) REVERT: B 69 PHE cc_start: 0.7300 (m-80) cc_final: 0.6552 (m-80) REVERT: B 82 LEU cc_start: 0.8859 (tp) cc_final: 0.8447 (tp) REVERT: B 100 PHE cc_start: 0.8632 (p90) cc_final: 0.8013 (p90) REVERT: B 105 ASP cc_start: 0.8960 (p0) cc_final: 0.8642 (p0) REVERT: B 110 TYR cc_start: 0.7682 (m-80) cc_final: 0.7449 (m-80) REVERT: E 31 LYS cc_start: 0.9522 (mtpp) cc_final: 0.9028 (mmmm) REVERT: E 34 THR cc_start: 0.8886 (m) cc_final: 0.8587 (m) REVERT: E 40 TYR cc_start: 0.9149 (t80) cc_final: 0.8873 (t80) REVERT: E 42 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8350 (tm-30) REVERT: E 85 GLU cc_start: 0.9048 (tt0) cc_final: 0.8670 (tm-30) REVERT: E 116 ARG cc_start: 0.8552 (mmt-90) cc_final: 0.8157 (mmm-85) REVERT: E 145 ASN cc_start: 0.9116 (m110) cc_final: 0.8817 (m110) REVERT: E 155 ASP cc_start: 0.8391 (p0) cc_final: 0.7971 (p0) REVERT: E 183 ASN cc_start: 0.9504 (p0) cc_final: 0.9202 (p0) REVERT: F 33 ARG cc_start: 0.9165 (ptm-80) cc_final: 0.8731 (ptm-80) REVERT: F 35 THR cc_start: 0.9262 (m) cc_final: 0.9026 (m) REVERT: F 69 PHE cc_start: 0.7583 (m-80) cc_final: 0.7080 (m-80) REVERT: F 82 LEU cc_start: 0.8864 (tp) cc_final: 0.8399 (tp) REVERT: F 105 ASP cc_start: 0.8979 (p0) cc_final: 0.8704 (p0) REVERT: F 110 TYR cc_start: 0.7737 (m-80) cc_final: 0.7392 (m-80) REVERT: G 14 GLU cc_start: 0.9173 (pm20) cc_final: 0.8904 (pm20) REVERT: G 34 THR cc_start: 0.8926 (m) cc_final: 0.8594 (m) REVERT: G 36 CYS cc_start: 0.7324 (m) cc_final: 0.6927 (m) REVERT: G 42 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8333 (tm-30) REVERT: G 62 GLU cc_start: 0.9100 (tp30) cc_final: 0.8748 (tp30) REVERT: G 85 GLU cc_start: 0.9016 (tt0) cc_final: 0.8611 (tm-30) REVERT: G 95 HIS cc_start: 0.8936 (t-170) cc_final: 0.8491 (t-170) REVERT: G 145 ASN cc_start: 0.9025 (m110) cc_final: 0.8679 (m110) REVERT: G 197 GLU cc_start: 0.8678 (tp30) cc_final: 0.8250 (tp30) REVERT: H 33 ARG cc_start: 0.9118 (ptm-80) cc_final: 0.8763 (ptm-80) REVERT: H 35 THR cc_start: 0.9250 (m) cc_final: 0.8656 (m) REVERT: H 82 LEU cc_start: 0.8646 (tp) cc_final: 0.8143 (tp) REVERT: H 100 PHE cc_start: 0.8649 (p90) cc_final: 0.7963 (p90) REVERT: H 101 ARG cc_start: 0.8262 (ptt90) cc_final: 0.7909 (ptt180) REVERT: H 105 ASP cc_start: 0.8872 (p0) cc_final: 0.8565 (p0) REVERT: H 110 TYR cc_start: 0.7811 (m-80) cc_final: 0.7495 (m-80) REVERT: I 31 LYS cc_start: 0.9498 (mtpp) cc_final: 0.8981 (mmmm) REVERT: I 36 CYS cc_start: 0.7267 (m) cc_final: 0.6886 (m) REVERT: I 42 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8332 (tm-30) REVERT: I 85 GLU cc_start: 0.8983 (tt0) cc_final: 0.8606 (tm-30) REVERT: I 95 HIS cc_start: 0.8730 (t-90) cc_final: 0.7979 (t-170) REVERT: I 145 ASN cc_start: 0.9052 (m110) cc_final: 0.8741 (m110) REVERT: I 163 ASP cc_start: 0.9238 (p0) cc_final: 0.8994 (p0) REVERT: I 183 ASN cc_start: 0.9517 (p0) cc_final: 0.9216 (p0) REVERT: J 33 ARG cc_start: 0.9084 (ptm-80) cc_final: 0.8713 (ptm-80) REVERT: J 47 ARG cc_start: 0.8072 (tpp80) cc_final: 0.7541 (tpp80) REVERT: J 82 LEU cc_start: 0.8657 (tp) cc_final: 0.8343 (tp) REVERT: J 96 TYR cc_start: 0.8666 (m-80) cc_final: 0.8459 (m-80) REVERT: J 105 ASP cc_start: 0.9011 (p0) cc_final: 0.8689 (p0) REVERT: J 110 TYR cc_start: 0.7600 (m-80) cc_final: 0.7328 (m-80) outliers start: 0 outliers final: 0 residues processed: 686 average time/residue: 0.2207 time to fit residues: 216.7222 Evaluate side-chains 632 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 632 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 70 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 154 optimal weight: 0.0770 chunk 51 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.064373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.049371 restraints weight = 93120.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.052965 restraints weight = 35799.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.055458 restraints weight = 18009.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.057065 restraints weight = 10444.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.058124 restraints weight = 6745.008| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 13090 Z= 0.264 Angle : 0.626 7.180 17770 Z= 0.339 Chirality : 0.044 0.166 1935 Planarity : 0.005 0.043 2265 Dihedral : 5.321 18.434 1770 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 62.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.09 % Favored : 88.91 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: -3.54 (0.19), residues: 1605 helix: 1.06 (0.61), residues: 55 sheet: -2.80 (0.21), residues: 530 loop : -2.36 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 47 TYR 0.019 0.002 TYR A 49 PHE 0.022 0.002 PHE E 75 TRP 0.016 0.002 TRP J 112 HIS 0.014 0.002 HIS I 38 Details of bonding type rmsd covalent geometry : bond 0.00551 (13085) covalent geometry : angle 0.62497 (17760) SS BOND : bond 0.00596 ( 5) SS BOND : angle 1.82103 ( 10) hydrogen bonds : bond 0.03852 ( 405) hydrogen bonds : angle 7.54901 ( 885) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 656 time to evaluate : 0.656 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 31 LYS cc_start: 0.9526 (mtpp) cc_final: 0.9014 (mmmm) REVERT: C 36 CYS cc_start: 0.7557 (m) cc_final: 0.7018 (m) REVERT: C 42 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8394 (tm-30) REVERT: C 57 LYS cc_start: 0.9603 (mmmm) cc_final: 0.9099 (mmmm) REVERT: C 85 GLU cc_start: 0.9176 (tt0) cc_final: 0.8716 (tm-30) REVERT: C 95 HIS cc_start: 0.8725 (t-90) cc_final: 0.7666 (t70) REVERT: C 116 ARG cc_start: 0.8544 (mmm-85) cc_final: 0.8262 (mmt90) REVERT: C 130 GLU cc_start: 0.7888 (pp20) cc_final: 0.7636 (pp20) REVERT: C 145 ASN cc_start: 0.9137 (m110) cc_final: 0.8811 (m110) REVERT: C 155 ASP cc_start: 0.8489 (p0) cc_final: 0.8212 (p0) REVERT: C 163 ASP cc_start: 0.9343 (p0) cc_final: 0.9126 (p0) REVERT: D 22 LEU cc_start: 0.9620 (mt) cc_final: 0.9301 (mt) REVERT: D 33 ARG cc_start: 0.9100 (ptm-80) cc_final: 0.8667 (ptm-80) REVERT: D 48 ASP cc_start: 0.9218 (t70) cc_final: 0.8973 (t0) REVERT: D 68 ARG cc_start: 0.7679 (mtp-110) cc_final: 0.7138 (mtp-110) REVERT: D 82 LEU cc_start: 0.8852 (tp) cc_final: 0.8394 (tp) REVERT: D 101 ARG cc_start: 0.8366 (ptt90) cc_final: 0.7545 (ptt180) REVERT: D 105 ASP cc_start: 0.8868 (p0) cc_final: 0.8552 (p0) REVERT: D 110 TYR cc_start: 0.7752 (m-80) cc_final: 0.7408 (m-80) REVERT: A 31 LYS cc_start: 0.9538 (mtpp) cc_final: 0.9040 (mmmm) REVERT: A 42 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8361 (tm-30) REVERT: A 85 GLU cc_start: 0.9151 (tt0) cc_final: 0.8631 (tm-30) REVERT: A 145 ASN cc_start: 0.9147 (m110) cc_final: 0.8821 (m110) REVERT: A 155 ASP cc_start: 0.8291 (p0) cc_final: 0.7912 (p0) REVERT: B 19 SER cc_start: 0.9322 (p) cc_final: 0.9112 (m) REVERT: B 22 LEU cc_start: 0.9682 (mt) cc_final: 0.8996 (mt) REVERT: B 33 ARG cc_start: 0.9115 (ptm-80) cc_final: 0.8687 (ptm-80) REVERT: B 35 THR cc_start: 0.9318 (m) cc_final: 0.8848 (m) REVERT: B 38 TRP cc_start: 0.8602 (m100) cc_final: 0.7625 (m-10) REVERT: B 48 ASP cc_start: 0.9230 (t70) cc_final: 0.9007 (t0) REVERT: B 71 ILE cc_start: 0.9375 (tp) cc_final: 0.8259 (tp) REVERT: B 82 LEU cc_start: 0.8912 (tp) cc_final: 0.8353 (tp) REVERT: B 100 PHE cc_start: 0.8576 (p90) cc_final: 0.7746 (p90) REVERT: B 105 ASP cc_start: 0.8884 (p0) cc_final: 0.8542 (p0) REVERT: B 110 TYR cc_start: 0.7664 (m-80) cc_final: 0.7411 (m-80) REVERT: E 31 LYS cc_start: 0.9538 (mtpp) cc_final: 0.9063 (mmmm) REVERT: E 34 THR cc_start: 0.8906 (m) cc_final: 0.8597 (m) REVERT: E 40 TYR cc_start: 0.9232 (t80) cc_final: 0.8952 (t80) REVERT: E 42 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8394 (tm-30) REVERT: E 57 LYS cc_start: 0.9609 (mmmm) cc_final: 0.9115 (mmmm) REVERT: E 85 GLU cc_start: 0.9036 (tt0) cc_final: 0.8621 (tm-30) REVERT: E 116 ARG cc_start: 0.8677 (mmt-90) cc_final: 0.8330 (mmm-85) REVERT: E 145 ASN cc_start: 0.9170 (m110) cc_final: 0.8868 (m110) REVERT: E 155 ASP cc_start: 0.8492 (p0) cc_final: 0.8093 (p0) REVERT: F 31 PHE cc_start: 0.8906 (m-10) cc_final: 0.8556 (m-10) REVERT: F 35 THR cc_start: 0.9311 (m) cc_final: 0.9106 (m) REVERT: F 68 ARG cc_start: 0.7609 (mtp-110) cc_final: 0.6638 (mtp-110) REVERT: F 82 LEU cc_start: 0.8975 (tp) cc_final: 0.8469 (tp) REVERT: F 105 ASP cc_start: 0.8978 (p0) cc_final: 0.8611 (p0) REVERT: G 14 GLU cc_start: 0.9154 (pm20) cc_final: 0.8913 (pm20) REVERT: G 31 LYS cc_start: 0.9544 (mtpp) cc_final: 0.9208 (mtpp) REVERT: G 36 CYS cc_start: 0.7321 (m) cc_final: 0.6917 (m) REVERT: G 42 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8375 (tm-30) REVERT: G 62 GLU cc_start: 0.9121 (tp30) cc_final: 0.7951 (tp30) REVERT: G 85 GLU cc_start: 0.9010 (tt0) cc_final: 0.8635 (tm-30) REVERT: G 109 PHE cc_start: 0.9296 (t80) cc_final: 0.9080 (t80) REVERT: G 123 LYS cc_start: 0.9553 (tmtt) cc_final: 0.9311 (tptm) REVERT: G 197 GLU cc_start: 0.8801 (tp30) cc_final: 0.8332 (tp30) REVERT: H 8 GLU cc_start: 0.8680 (pm20) cc_final: 0.8147 (pm20) REVERT: H 22 LEU cc_start: 0.9606 (mt) cc_final: 0.9197 (mt) REVERT: H 33 ARG cc_start: 0.9124 (ptm-80) cc_final: 0.8639 (ptm-80) REVERT: H 35 THR cc_start: 0.9188 (m) cc_final: 0.8743 (m) REVERT: H 38 TRP cc_start: 0.8325 (m100) cc_final: 0.8014 (m100) REVERT: H 48 ASP cc_start: 0.9265 (t70) cc_final: 0.9053 (t0) REVERT: H 82 LEU cc_start: 0.8753 (tp) cc_final: 0.8137 (tp) REVERT: H 100 PHE cc_start: 0.8708 (p90) cc_final: 0.7898 (p90) REVERT: H 101 ARG cc_start: 0.8364 (ptt90) cc_final: 0.7634 (ptt180) REVERT: H 110 TYR cc_start: 0.7769 (m-80) cc_final: 0.7495 (m-80) REVERT: I 31 LYS cc_start: 0.9521 (mtpp) cc_final: 0.9019 (mmmm) REVERT: I 36 CYS cc_start: 0.7351 (m) cc_final: 0.6886 (m) REVERT: I 42 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8391 (tm-30) REVERT: I 57 LYS cc_start: 0.9603 (mmmm) cc_final: 0.9320 (mmmt) REVERT: I 85 GLU cc_start: 0.8986 (tt0) cc_final: 0.8712 (tm-30) REVERT: I 95 HIS cc_start: 0.8771 (t-90) cc_final: 0.8169 (t-90) REVERT: I 130 GLU cc_start: 0.7914 (pp20) cc_final: 0.7617 (pp20) REVERT: I 145 ASN cc_start: 0.9092 (m110) cc_final: 0.8780 (m110) REVERT: J 31 PHE cc_start: 0.8650 (m-10) cc_final: 0.8303 (m-10) REVERT: J 35 THR cc_start: 0.9232 (m) cc_final: 0.8970 (m) REVERT: J 54 THR cc_start: 0.8775 (p) cc_final: 0.8282 (p) REVERT: J 82 LEU cc_start: 0.8878 (tp) cc_final: 0.8436 (tp) outliers start: 0 outliers final: 0 residues processed: 656 average time/residue: 0.2248 time to fit residues: 210.8620 Evaluate side-chains 607 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 607 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN E 160 ASN ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 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 = 0.3025 r_free = 0.3025 target = 0.067673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.052232 restraints weight = 89524.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.056033 restraints weight = 34144.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.058640 restraints weight = 17082.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.060338 restraints weight = 9801.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.061407 restraints weight = 6207.414| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13090 Z= 0.148 Angle : 0.577 6.481 17770 Z= 0.314 Chirality : 0.044 0.150 1935 Planarity : 0.004 0.036 2265 Dihedral : 5.117 19.422 1770 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 52.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -3.37 (0.19), residues: 1605 helix: 1.21 (0.65), residues: 55 sheet: -2.66 (0.22), residues: 490 loop : -2.32 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 68 TYR 0.018 0.002 TYR C 54 PHE 0.023 0.002 PHE F 69 TRP 0.014 0.002 TRP F 112 HIS 0.012 0.002 HIS E 38 Details of bonding type rmsd covalent geometry : bond 0.00332 (13085) covalent geometry : angle 0.57590 (17760) SS BOND : bond 0.00394 ( 5) SS BOND : angle 1.31009 ( 10) hydrogen bonds : bond 0.03379 ( 405) hydrogen bonds : angle 7.35630 ( 885) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 677 time to evaluate : 0.653 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: C 31 LYS cc_start: 0.9497 (mtpp) cc_final: 0.8979 (mmmm) REVERT: C 34 THR cc_start: 0.8913 (m) cc_final: 0.8574 (m) REVERT: C 36 CYS cc_start: 0.7545 (m) cc_final: 0.7020 (m) REVERT: C 42 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8344 (tm-30) REVERT: C 57 LYS cc_start: 0.9568 (mmmm) cc_final: 0.9054 (mmmm) REVERT: C 85 GLU cc_start: 0.9152 (tt0) cc_final: 0.8686 (tm-30) REVERT: C 95 HIS cc_start: 0.8776 (t-90) cc_final: 0.7727 (t-170) REVERT: C 116 ARG cc_start: 0.8499 (mmm-85) cc_final: 0.8258 (mmt90) REVERT: C 130 GLU cc_start: 0.7863 (pp20) cc_final: 0.7571 (pp20) REVERT: C 145 ASN cc_start: 0.9132 (m110) cc_final: 0.8811 (m110) REVERT: D 22 LEU cc_start: 0.9534 (mt) cc_final: 0.9077 (mt) REVERT: D 24 CYS cc_start: 0.8639 (t) cc_final: 0.8295 (t) REVERT: D 33 ARG cc_start: 0.9111 (ptm-80) cc_final: 0.8904 (ptp90) REVERT: D 35 THR cc_start: 0.9180 (m) cc_final: 0.8972 (m) REVERT: D 38 TRP cc_start: 0.8472 (m100) cc_final: 0.7926 (m100) REVERT: D 48 ASP cc_start: 0.9178 (t70) cc_final: 0.8884 (t70) REVERT: D 68 ARG cc_start: 0.7765 (mtp-110) cc_final: 0.7198 (mtp-110) REVERT: D 82 LEU cc_start: 0.8447 (tp) cc_final: 0.8136 (tp) REVERT: D 87 LEU cc_start: 0.8511 (mt) cc_final: 0.8180 (mt) REVERT: D 101 ARG cc_start: 0.8090 (ptt90) cc_final: 0.7861 (ptt180) REVERT: D 105 ASP cc_start: 0.8906 (p0) cc_final: 0.8620 (p0) REVERT: D 110 TYR cc_start: 0.7768 (m-80) cc_final: 0.7511 (m-80) REVERT: A 31 LYS cc_start: 0.9513 (mtpp) cc_final: 0.8999 (mmmm) REVERT: A 42 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8285 (tm-30) REVERT: A 85 GLU cc_start: 0.8997 (tt0) cc_final: 0.8584 (tm-30) REVERT: A 95 HIS cc_start: 0.8774 (t-170) cc_final: 0.8564 (t70) REVERT: A 112 ASP cc_start: 0.8938 (t0) cc_final: 0.8724 (t0) REVERT: A 145 ASN cc_start: 0.9150 (m110) cc_final: 0.8802 (m110) REVERT: A 155 ASP cc_start: 0.8191 (p0) cc_final: 0.7811 (p0) REVERT: B 22 LEU cc_start: 0.9705 (mt) cc_final: 0.9397 (mt) REVERT: B 35 THR cc_start: 0.9280 (m) cc_final: 0.9068 (m) REVERT: B 48 ASP cc_start: 0.9183 (t70) cc_final: 0.8961 (t0) REVERT: B 68 ARG cc_start: 0.7893 (mtp-110) cc_final: 0.7367 (mtp-110) REVERT: B 82 LEU cc_start: 0.8881 (tp) cc_final: 0.8468 (tp) REVERT: E 31 LYS cc_start: 0.9508 (mtpp) cc_final: 0.9016 (mmmm) REVERT: E 34 THR cc_start: 0.8858 (m) cc_final: 0.8570 (m) REVERT: E 57 LYS cc_start: 0.9573 (mmmm) cc_final: 0.9066 (mmmm) REVERT: E 67 TRP cc_start: 0.9241 (t-100) cc_final: 0.8755 (t-100) REVERT: E 85 GLU cc_start: 0.8991 (tt0) cc_final: 0.8586 (tm-30) REVERT: E 95 HIS cc_start: 0.9006 (t-170) cc_final: 0.8744 (t70) REVERT: E 145 ASN cc_start: 0.9190 (m110) cc_final: 0.8868 (m110) REVERT: E 155 ASP cc_start: 0.8398 (p0) cc_final: 0.8022 (p0) REVERT: E 163 ASP cc_start: 0.9296 (p0) cc_final: 0.9082 (p0) REVERT: E 183 ASN cc_start: 0.9492 (p0) cc_final: 0.9188 (p0) REVERT: F 35 THR cc_start: 0.9224 (m) cc_final: 0.8937 (m) REVERT: F 54 THR cc_start: 0.8985 (p) cc_final: 0.8567 (p) REVERT: F 68 ARG cc_start: 0.8012 (mtp-110) cc_final: 0.7392 (mtp-110) REVERT: F 82 LEU cc_start: 0.8958 (tp) cc_final: 0.8513 (tp) REVERT: F 105 ASP cc_start: 0.8920 (p0) cc_final: 0.8660 (p0) REVERT: F 110 TYR cc_start: 0.7681 (m-80) cc_final: 0.7464 (m-80) REVERT: G 14 GLU cc_start: 0.9169 (pm20) cc_final: 0.8906 (pm20) REVERT: G 26 LEU cc_start: 0.8132 (tp) cc_final: 0.7901 (tp) REVERT: G 36 CYS cc_start: 0.7161 (m) cc_final: 0.6899 (m) REVERT: G 37 LEU cc_start: 0.9561 (pp) cc_final: 0.9348 (pp) REVERT: G 42 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8302 (tm-30) REVERT: G 57 LYS cc_start: 0.9555 (mmmm) cc_final: 0.9040 (mmmm) REVERT: G 62 GLU cc_start: 0.9105 (tp30) cc_final: 0.8762 (tp30) REVERT: G 85 GLU cc_start: 0.8979 (tt0) cc_final: 0.8551 (tm-30) REVERT: G 95 HIS cc_start: 0.8907 (t-170) cc_final: 0.8355 (t70) REVERT: G 109 PHE cc_start: 0.9295 (t80) cc_final: 0.8978 (t80) REVERT: G 123 LYS cc_start: 0.9530 (tmtt) cc_final: 0.9284 (tptm) REVERT: G 145 ASN cc_start: 0.9073 (m110) cc_final: 0.8721 (m110) REVERT: G 197 GLU cc_start: 0.8794 (tp30) cc_final: 0.8372 (tp30) REVERT: H 8 GLU cc_start: 0.8700 (pm20) cc_final: 0.8170 (pm20) REVERT: H 33 ARG cc_start: 0.9115 (ptm-80) cc_final: 0.8653 (ptm-80) REVERT: H 35 THR cc_start: 0.9178 (m) cc_final: 0.8721 (m) REVERT: H 48 ASP cc_start: 0.9223 (t70) cc_final: 0.8963 (t70) REVERT: H 68 ARG cc_start: 0.8078 (mtp-110) cc_final: 0.7681 (mtp-110) REVERT: H 82 LEU cc_start: 0.8770 (tp) cc_final: 0.8395 (tp) REVERT: H 100 PHE cc_start: 0.8547 (p90) cc_final: 0.7891 (p90) REVERT: H 101 ARG cc_start: 0.8239 (ptt90) cc_final: 0.7657 (ptt180) REVERT: H 105 ASP cc_start: 0.8935 (p0) cc_final: 0.8536 (p0) REVERT: H 110 TYR cc_start: 0.7777 (m-80) cc_final: 0.7445 (m-80) REVERT: I 2 THR cc_start: 0.9367 (m) cc_final: 0.9166 (p) REVERT: I 31 LYS cc_start: 0.9493 (mtpp) cc_final: 0.8989 (mmmm) REVERT: I 36 CYS cc_start: 0.7350 (m) cc_final: 0.6868 (m) REVERT: I 42 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8293 (tm-30) REVERT: I 57 LYS cc_start: 0.9566 (mmmm) cc_final: 0.9333 (mmmm) REVERT: I 85 GLU cc_start: 0.8979 (tt0) cc_final: 0.8603 (tm-30) REVERT: I 95 HIS cc_start: 0.8755 (t-90) cc_final: 0.8111 (t-90) REVERT: I 145 ASN cc_start: 0.9051 (m110) cc_final: 0.8740 (m110) REVERT: I 163 ASP cc_start: 0.9227 (p0) cc_final: 0.8992 (p0) REVERT: I 183 ASN cc_start: 0.9520 (p0) cc_final: 0.9206 (p0) REVERT: J 33 ARG cc_start: 0.8995 (ptm-80) cc_final: 0.8454 (ptm-80) REVERT: J 47 ARG cc_start: 0.8115 (tpp80) cc_final: 0.7891 (tpp80) REVERT: J 87 LEU cc_start: 0.8443 (mt) cc_final: 0.8143 (mt) REVERT: J 110 TYR cc_start: 0.7565 (m-80) cc_final: 0.7268 (m-80) outliers start: 0 outliers final: 0 residues processed: 677 average time/residue: 0.2176 time to fit residues: 211.7336 Evaluate side-chains 644 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 644 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 137 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 123 optimal weight: 0.0980 chunk 103 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 114 optimal weight: 0.3980 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 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 = 0.3016 r_free = 0.3016 target = 0.067498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.052188 restraints weight = 90359.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.055939 restraints weight = 34230.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.058485 restraints weight = 17102.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.060218 restraints weight = 9883.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.061322 restraints weight = 6287.911| |-----------------------------------------------------------------------------| r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13090 Z= 0.164 Angle : 0.561 6.763 17770 Z= 0.305 Chirality : 0.044 0.145 1935 Planarity : 0.004 0.045 2265 Dihedral : 5.083 17.976 1770 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 52.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -3.20 (0.19), residues: 1605 helix: 1.30 (0.66), residues: 55 sheet: -2.59 (0.20), residues: 580 loop : -2.04 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 68 TYR 0.032 0.002 TYR E 40 PHE 0.018 0.002 PHE E 75 TRP 0.015 0.001 TRP F 112 HIS 0.010 0.002 HIS I 38 Details of bonding type rmsd covalent geometry : bond 0.00364 (13085) covalent geometry : angle 0.55985 (17760) SS BOND : bond 0.00442 ( 5) SS BOND : angle 1.47543 ( 10) hydrogen bonds : bond 0.03334 ( 405) hydrogen bonds : angle 7.26639 ( 885) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4638.62 seconds wall clock time: 80 minutes 38.56 seconds (4838.56 seconds total)