Starting phenix.real_space_refine on Wed Aug 5 21:04:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fya_29562/08_2026/8fya_29562.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fya_29562/08_2026/8fya_29562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fya_29562/08_2026/8fya_29562.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fya_29562/08_2026/8fya_29562.map" model { file = "/net/cci-nas-00/data/ceres_data/8fya_29562/08_2026/8fya_29562.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fya_29562/08_2026/8fya_29562.cif" } resolution = 2.91 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= -0.000 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 611 atoms to isotropic. 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 P 57 5.49 5 S 31 5.16 5 C 7056 2.51 5 N 2060 2.21 5 O 2229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11433 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 746 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "B" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2295 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain: "C" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2388 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain breaks: 1 Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 746 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "E" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1865 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 8, 'TRANS': 232} Chain breaks: 1 Chain: "F" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2186 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain: "G" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 573 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "H" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Time building chain proxies: 2.20, per 1000 atoms: 0.19 Number of scatterers: 11433 At special positions: 0 Unit cell: (93.66, 90.315, 142.72, 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 31 16.00 P 57 15.00 O 2229 8.00 N 2060 7.00 C 7056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 375.6 milliseconds 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2410 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 8 sheets defined 51.2% alpha, 15.4% beta 20 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 Processing helix chain 'A' and resid 20 through 22 No H-bonds generated for 'chain 'A' and resid 20 through 22' Processing helix chain 'A' and resid 36 through 49 removed outlier: 3.823A pdb=" N GLU A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 55 Processing helix chain 'B' and resid 67 through 77 Processing helix chain 'B' and resid 86 through 89 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 102 through 114 removed outlier: 3.982A pdb=" N ASN B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 129 Processing helix chain 'B' and resid 139 through 163 Processing helix chain 'B' and resid 180 through 205 Processing helix chain 'B' and resid 219 through 231 removed outlier: 3.872A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 250 through 265 removed outlier: 4.343A pdb=" N ASP B 265 " --> pdb=" O ASP B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 280 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.871A pdb=" N ARG C 21 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 53 No H-bonds generated for 'chain 'C' and resid 51 through 53' Processing helix chain 'C' and resid 68 through 77 Processing helix chain 'C' and resid 102 through 114 removed outlier: 3.517A pdb=" N ASN C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 130 Processing helix chain 'C' and resid 139 through 163 Processing helix chain 'C' and resid 180 through 205 Processing helix chain 'C' and resid 219 through 231 removed outlier: 3.722A pdb=" N LEU C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.507A pdb=" N LEU C 254 " --> pdb=" O ASP C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 280 removed outlier: 3.539A pdb=" N LEU C 280 " --> pdb=" O LEU C 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 19 Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 36 through 49 Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 68 through 77 Processing helix chain 'E' and resid 86 through 89 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 102 through 114 removed outlier: 3.999A pdb=" N ASN E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 129 removed outlier: 3.581A pdb=" N ARG E 118 " --> pdb=" O ASN E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 205 Processing helix chain 'E' and resid 219 through 231 removed outlier: 3.806A pdb=" N LEU E 228 " --> pdb=" O ASP E 224 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA E 231 " --> pdb=" O ASP E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 245 Processing helix chain 'E' and resid 250 through 265 removed outlier: 4.451A pdb=" N ASP E 265 " --> pdb=" O ASP E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 280 removed outlier: 3.648A pdb=" N LEU E 280 " --> pdb=" O LEU E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 303 Processing helix chain 'F' and resid 51 through 53 No H-bonds generated for 'chain 'F' and resid 51 through 53' Processing helix chain 'F' and resid 68 through 78 Processing helix chain 'F' and resid 102 through 114 removed outlier: 3.881A pdb=" N ASN F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 130 Processing helix chain 'F' and resid 139 through 163 Processing helix chain 'F' and resid 180 through 205 Processing helix chain 'F' and resid 219 through 231 removed outlier: 3.758A pdb=" N LEU F 228 " --> pdb=" O ASP F 224 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR F 229 " --> pdb=" O VAL F 225 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA F 231 " --> pdb=" O ASP F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 245 Processing helix chain 'F' and resid 250 through 267 Processing helix chain 'F' and resid 267 through 280 removed outlier: 3.868A pdb=" N LEU F 280 " --> pdb=" O LEU F 276 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 5.798A pdb=" N GLU A 25 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL A 32 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA A 27 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N MET A 3 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA A 61 " --> pdb=" O MET A 3 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 56 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81 removed outlier: 5.461A pdb=" N ILE A 88 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG F 49 " --> pdb=" O ILE A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 289 through 291 removed outlier: 8.105A pdb=" N VAL B 57 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR B 23 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU B 59 " --> pdb=" O THR B 23 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE B 25 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU B 58 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL B 84 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU B 60 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER B 94 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP B 83 " --> pdb=" O TYR B 92 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR C 91 " --> pdb=" O TRP C 83 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR C 23 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LEU C 59 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE C 25 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 308 through 310 removed outlier: 3.901A pdb=" N ASN B 308 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ALA B 30 " --> pdb=" O ASP B 65 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG C 34 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG C 49 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE D 88 " --> pdb=" O ARG C 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 214 through 215 Processing sheet with id=AA6, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.287A pdb=" N VAL D 30 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N MET D 3 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA D 61 " --> pdb=" O MET D 3 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 289 through 291 removed outlier: 7.715A pdb=" N VAL E 57 " --> pdb=" O ARG E 21 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N THR E 23 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU E 59 " --> pdb=" O THR E 23 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE E 25 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR F 91 " --> pdb=" O TRP F 83 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR F 23 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU F 59 " --> pdb=" O THR F 23 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE F 25 " --> pdb=" O LEU F 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 308 through 310 removed outlier: 7.598A pdb=" N ILE E 32 " --> pdb=" O SER E 67 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1638 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 1.90 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3360 1.34 - 1.45: 2039 1.45 - 1.57: 6193 1.57 - 1.69: 114 1.69 - 1.81: 60 Bond restraints: 11766 Sorted by residual: bond pdb=" C3' DT H 9 " pdb=" C2' DT H 9 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C3' DT H 30 " pdb=" C2' DT H 30 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DA G 21 " pdb=" C2' DA G 21 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DT H 3 " pdb=" C2' DT H 3 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DC G 17 " pdb=" C2' DC G 17 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 11761 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 15467 1.20 - 2.41: 566 2.41 - 3.61: 118 3.61 - 4.81: 12 4.81 - 6.02: 11 Bond angle restraints: 16174 Sorted by residual: angle pdb=" O4' DA G 25 " pdb=" C4' DA G 25 " pdb=" C3' DA G 25 " ideal model delta sigma weight residual 106.00 103.37 2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT H 20 " pdb=" C4 DT H 20 " pdb=" O4 DT H 20 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT H 9 " pdb=" C4 DT H 9 " pdb=" O4 DT H 9 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT H 30 " pdb=" C4 DT H 30 " pdb=" O4 DT H 30 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT H 3 " pdb=" C4 DT H 3 " pdb=" O4 DT H 3 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 ... (remaining 16169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 6645 35.99 - 71.98: 279 71.98 - 107.97: 9 107.97 - 143.96: 0 143.96 - 179.96: 1 Dihedral angle restraints: 6934 sinusoidal: 3177 harmonic: 3757 Sorted by residual: dihedral pdb=" C4' DC G 8 " pdb=" C3' DC G 8 " pdb=" O3' DC G 8 " pdb=" P DT G 9 " ideal model delta sinusoidal sigma weight residual -140.00 39.96 -179.96 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA ARG E 34 " pdb=" C ARG E 34 " pdb=" N VAL E 35 " pdb=" CA VAL E 35 " ideal model delta harmonic sigma weight residual 180.00 160.93 19.07 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLU F 19 " pdb=" C GLU F 19 " pdb=" N ASP F 20 " pdb=" CA ASP F 20 " ideal model delta harmonic sigma weight residual -180.00 -161.21 -18.79 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 6931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1248 0.037 - 0.074: 395 0.074 - 0.110: 142 0.110 - 0.147: 36 0.147 - 0.184: 2 Chirality restraints: 1823 Sorted by residual: chirality pdb=" CB VAL C 191 " pdb=" CA VAL C 191 " pdb=" CG1 VAL C 191 " pdb=" CG2 VAL C 191 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CA ILE B 50 " pdb=" N ILE B 50 " pdb=" C ILE B 50 " pdb=" CB ILE B 50 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CB THR E 113 " pdb=" CA THR E 113 " pdb=" OG1 THR E 113 " pdb=" CG2 THR E 113 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 1820 not shown) Planarity restraints: 1879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 172 " -0.025 5.00e-02 4.00e+02 3.91e-02 2.44e+00 pdb=" N PRO B 173 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 173 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 173 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 85 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO D 86 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 86 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 86 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 31 " -0.009 2.00e-02 2.50e+03 9.37e-03 1.76e+00 pdb=" CG TYR A 31 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR A 31 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 31 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 31 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 31 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 31 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 31 " 0.000 2.00e-02 2.50e+03 ... (remaining 1876 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 492 2.72 - 3.26: 11148 3.26 - 3.81: 20453 3.81 - 4.35: 25083 4.35 - 4.90: 41575 Nonbonded interactions: 98751 Sorted by model distance: nonbonded pdb=" OH TYR F 229 " pdb=" OD2 ASP F 275 " model vdw 2.172 3.040 nonbonded pdb=" OH TYR E 229 " pdb=" OD2 ASP E 275 " model vdw 2.174 3.040 nonbonded pdb=" OG1 THR A 7 " pdb=" OG SER A 57 " model vdw 2.201 3.040 nonbonded pdb=" O LEU E 295 " pdb=" OH TYR E 309 " model vdw 2.207 3.040 nonbonded pdb=" O GLY D 17 " pdb=" OG1 THR D 20 " model vdw 2.213 3.040 ... (remaining 98746 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = (chain 'B' and resid 20 through 283) selection = (chain 'C' and resid 20 through 283) selection = (chain 'F' and resid 20 through 283) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.550 Find NCS groups from input model: 0.160 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:5.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11766 Z= 0.280 Angle : 0.556 6.016 16174 Z= 0.387 Chirality : 0.043 0.184 1823 Planarity : 0.003 0.047 1879 Dihedral : 16.989 179.956 4524 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.09 % Allowed : 0.00 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.24), residues: 1288 helix: 2.15 (0.21), residues: 601 sheet: 0.05 (0.40), residues: 201 loop : -0.49 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 124 TYR 0.022 0.001 TYR A 31 PHE 0.008 0.001 PHE A 35 TRP 0.005 0.001 TRP E 83 HIS 0.010 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.28 (11766) covalent geometry : angle 0.55620 / 0.39 (16174) hydrogen bonds : bond 0.16746 / 11.14 ( 621) hydrogen bonds : angle 6.58993 / 4.64 ( 1724) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 244 time to evaluate : 0.253 Fit side-chains REVERT: A 58 MET cc_start: 0.8838 (ttp) cc_final: 0.8525 (ttp) REVERT: C 257 LEU cc_start: 0.8442 (tt) cc_final: 0.7867 (tp) REVERT: F 254 LEU cc_start: 0.8295 (tt) cc_final: 0.8083 (tt) outliers start: 1 outliers final: 1 residues processed: 244 average time/residue: 0.5016 time to fit residues: 132.4288 Evaluate side-chains 180 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN C 33 ASN F 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.156182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.124438 restraints weight = 12449.609| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.76 r_work: 0.3316 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11766 Z= 0.210 Angle : 0.617 8.402 16174 Z= 0.342 Chirality : 0.045 0.254 1823 Planarity : 0.005 0.039 1879 Dihedral : 18.433 179.309 2097 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.63 % Allowed : 12.01 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.24), residues: 1288 helix: 2.00 (0.21), residues: 607 sheet: -0.20 (0.38), residues: 206 loop : -0.58 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 69 TYR 0.021 0.002 TYR A 31 PHE 0.015 0.002 PHE D 89 TRP 0.009 0.001 TRP B 296 HIS 0.013 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 (11766) covalent geometry : angle 0.61695 / 0.34 (16174) hydrogen bonds : bond 0.05950 / 4.03 ( 621) hydrogen bonds : angle 4.84821 / 3.43 ( 1724) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.347 Fit side-chains REVERT: A 71 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8343 (mt) REVERT: B 302 LEU cc_start: 0.8366 (mt) cc_final: 0.8090 (mm) REVERT: C 257 LEU cc_start: 0.8332 (tt) cc_final: 0.8061 (tt) REVERT: D 31 TYR cc_start: 0.8539 (m-80) cc_final: 0.8219 (m-80) REVERT: E 31 LYS cc_start: 0.8204 (mtpm) cc_final: 0.7808 (mtpt) REVERT: E 244 GLU cc_start: 0.7710 (tt0) cc_final: 0.7374 (tt0) REVERT: E 289 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.5470 (pp20) outliers start: 28 outliers final: 14 residues processed: 206 average time/residue: 0.4329 time to fit residues: 97.0290 Evaluate side-chains 183 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 127 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 20 optimal weight: 0.2980 chunk 61 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN F 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.158177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.126995 restraints weight = 12464.963| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.75 r_work: 0.3351 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11766 Z= 0.145 Angle : 0.545 7.128 16174 Z= 0.305 Chirality : 0.042 0.246 1823 Planarity : 0.004 0.035 1879 Dihedral : 18.618 179.956 2097 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.19 % Allowed : 14.17 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.24), residues: 1288 helix: 2.14 (0.21), residues: 608 sheet: -0.36 (0.37), residues: 206 loop : -0.53 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 69 TYR 0.010 0.001 TYR F 126 PHE 0.011 0.001 PHE D 89 TRP 0.009 0.001 TRP B 296 HIS 0.009 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (11766) covalent geometry : angle 0.54489 / 0.31 (16174) hydrogen bonds : bond 0.05023 / 3.44 ( 621) hydrogen bonds : angle 4.53815 / 3.22 ( 1724) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 0.396 Fit side-chains REVERT: A 58 MET cc_start: 0.9073 (ttp) cc_final: 0.8699 (ttp) REVERT: B 302 LEU cc_start: 0.8321 (mt) cc_final: 0.8062 (mm) REVERT: C 17 ARG cc_start: 0.7961 (mtp85) cc_final: 0.7634 (mtm-85) REVERT: C 257 LEU cc_start: 0.8266 (tt) cc_final: 0.7932 (tp) REVERT: D 10 ASN cc_start: 0.7309 (t0) cc_final: 0.7020 (m-40) REVERT: D 31 TYR cc_start: 0.8524 (m-80) cc_final: 0.8245 (m-80) REVERT: E 31 LYS cc_start: 0.8110 (mtpm) cc_final: 0.7828 (mtpp) REVERT: E 33 ASN cc_start: 0.7836 (OUTLIER) cc_final: 0.7547 (m-40) REVERT: E 244 GLU cc_start: 0.7670 (tt0) cc_final: 0.7379 (tt0) REVERT: F 121 VAL cc_start: 0.8010 (t) cc_final: 0.7763 (t) outliers start: 34 outliers final: 14 residues processed: 199 average time/residue: 0.4496 time to fit residues: 97.4035 Evaluate side-chains 190 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 123 optimal weight: 3.9990 chunk 18 optimal weight: 0.0970 chunk 93 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN ** C 33 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 = 0.3859 r_free = 0.3859 target = 0.158134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.126889 restraints weight = 12443.558| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.75 r_work: 0.3350 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11766 Z= 0.144 Angle : 0.535 6.787 16174 Z= 0.300 Chirality : 0.042 0.249 1823 Planarity : 0.004 0.033 1879 Dihedral : 18.633 179.709 2095 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.38 % Allowed : 15.10 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.24), residues: 1288 helix: 2.21 (0.21), residues: 610 sheet: -0.41 (0.36), residues: 206 loop : -0.52 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 21 TYR 0.008 0.001 TYR E 229 PHE 0.013 0.001 PHE F 263 TRP 0.009 0.001 TRP B 296 HIS 0.008 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (11766) covalent geometry : angle 0.53456 / 0.30 (16174) hydrogen bonds : bond 0.04774 / 3.29 ( 621) hydrogen bonds : angle 4.39550 / 3.13 ( 1724) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 0.246 Fit side-chains REVERT: A 58 MET cc_start: 0.9071 (ttp) cc_final: 0.8680 (ttp) REVERT: B 302 LEU cc_start: 0.8382 (mt) cc_final: 0.8147 (mm) REVERT: C 17 ARG cc_start: 0.7938 (mtp85) cc_final: 0.7612 (mtm-85) REVERT: C 232 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7575 (pp20) REVERT: C 257 LEU cc_start: 0.8247 (tt) cc_final: 0.7960 (tp) REVERT: D 23 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8531 (ptm) REVERT: D 31 TYR cc_start: 0.8529 (m-80) cc_final: 0.8159 (m-80) REVERT: E 31 LYS cc_start: 0.8095 (mtpm) cc_final: 0.7824 (mtmm) REVERT: E 33 ASN cc_start: 0.7802 (OUTLIER) cc_final: 0.7556 (m-40) REVERT: E 76 ASP cc_start: 0.7726 (m-30) cc_final: 0.6986 (m-30) REVERT: E 244 GLU cc_start: 0.7628 (tt0) cc_final: 0.7340 (tt0) REVERT: E 270 LYS cc_start: 0.7889 (mtpp) cc_final: 0.7660 (mtpt) REVERT: E 271 ARG cc_start: 0.7716 (mtm110) cc_final: 0.7516 (mtm110) REVERT: E 289 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.5397 (pp20) REVERT: F 90 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7991 (mmm160) REVERT: F 121 VAL cc_start: 0.7947 (t) cc_final: 0.7704 (t) REVERT: F 138 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6168 (tt) REVERT: F 253 GLN cc_start: 0.8142 (tm-30) cc_final: 0.7875 (tm-30) REVERT: F 277 GLN cc_start: 0.8423 (tt0) cc_final: 0.8190 (tt0) outliers start: 36 outliers final: 17 residues processed: 207 average time/residue: 0.4685 time to fit residues: 105.4837 Evaluate side-chains 188 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 90 ARG Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 59 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN E 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.157712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.126405 restraints weight = 12476.919| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.76 r_work: 0.3336 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11766 Z= 0.148 Angle : 0.533 6.364 16174 Z= 0.298 Chirality : 0.042 0.249 1823 Planarity : 0.004 0.045 1879 Dihedral : 18.700 179.662 2095 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.47 % Allowed : 15.20 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.24), residues: 1288 helix: 2.26 (0.21), residues: 610 sheet: -0.32 (0.37), residues: 201 loop : -0.56 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 21 TYR 0.009 0.001 TYR F 126 PHE 0.014 0.001 PHE F 263 TRP 0.009 0.001 TRP B 296 HIS 0.008 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (11766) covalent geometry : angle 0.53327 / 0.30 (16174) hydrogen bonds : bond 0.04705 / 3.23 ( 621) hydrogen bonds : angle 4.32206 / 3.08 ( 1724) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 0.402 Fit side-chains REVERT: A 58 MET cc_start: 0.9091 (ttp) cc_final: 0.8688 (ttp) REVERT: C 17 ARG cc_start: 0.7925 (mtp85) cc_final: 0.7602 (mtm-85) REVERT: C 232 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7361 (pp20) REVERT: C 257 LEU cc_start: 0.8244 (tt) cc_final: 0.8002 (tp) REVERT: D 3 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7603 (ttt) REVERT: D 23 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8532 (ptm) REVERT: D 31 TYR cc_start: 0.8511 (m-80) cc_final: 0.8180 (m-80) REVERT: E 31 LYS cc_start: 0.8142 (mtpm) cc_final: 0.7822 (mtpp) REVERT: E 33 ASN cc_start: 0.7817 (OUTLIER) cc_final: 0.7572 (m-40) REVERT: E 244 GLU cc_start: 0.7672 (tt0) cc_final: 0.7393 (tt0) REVERT: E 270 LYS cc_start: 0.7845 (mtpp) cc_final: 0.7596 (mtpt) REVERT: E 289 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.5375 (pp20) REVERT: F 138 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6094 (tt) REVERT: F 253 GLN cc_start: 0.8202 (tm-30) cc_final: 0.7913 (tm-30) REVERT: F 277 GLN cc_start: 0.8436 (tt0) cc_final: 0.8203 (tt0) outliers start: 37 outliers final: 21 residues processed: 197 average time/residue: 0.4744 time to fit residues: 101.8916 Evaluate side-chains 199 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 102 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN E 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.157889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126332 restraints weight = 12483.056| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.80 r_work: 0.3337 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11766 Z= 0.145 Angle : 0.533 6.674 16174 Z= 0.296 Chirality : 0.042 0.251 1823 Planarity : 0.004 0.037 1879 Dihedral : 18.751 179.626 2095 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.66 % Allowed : 15.85 % Favored : 80.49 % 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: 1.24 (0.24), residues: 1288 helix: 2.28 (0.20), residues: 609 sheet: -0.31 (0.36), residues: 201 loop : -0.56 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 21 TYR 0.009 0.001 TYR A 31 PHE 0.011 0.001 PHE F 263 TRP 0.009 0.001 TRP B 296 HIS 0.007 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (11766) covalent geometry : angle 0.53316 / 0.30 (16174) hydrogen bonds : bond 0.04619 / 3.18 ( 621) hydrogen bonds : angle 4.26314 / 3.04 ( 1724) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 187 time to evaluate : 0.262 Fit side-chains REVERT: A 58 MET cc_start: 0.9100 (ttp) cc_final: 0.8676 (ttp) REVERT: B 302 LEU cc_start: 0.8243 (mt) cc_final: 0.8042 (mm) REVERT: C 17 ARG cc_start: 0.7901 (mtp85) cc_final: 0.7545 (mtm-85) REVERT: C 257 LEU cc_start: 0.8143 (tt) cc_final: 0.7918 (tp) REVERT: D 23 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8562 (ptm) REVERT: E 31 LYS cc_start: 0.8099 (mtpm) cc_final: 0.7775 (mtpp) REVERT: E 33 ASN cc_start: 0.7807 (OUTLIER) cc_final: 0.7543 (m-40) REVERT: E 244 GLU cc_start: 0.7682 (tt0) cc_final: 0.7360 (tt0) REVERT: E 270 LYS cc_start: 0.7739 (mtpp) cc_final: 0.7419 (mtpt) REVERT: E 289 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.5458 (pp20) REVERT: F 72 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: F 138 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6076 (tt) REVERT: F 140 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.7142 (tpp) REVERT: F 257 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7825 (mt) REVERT: F 277 GLN cc_start: 0.8413 (tt0) cc_final: 0.8167 (tt0) outliers start: 39 outliers final: 20 residues processed: 208 average time/residue: 0.4285 time to fit residues: 97.5165 Evaluate side-chains 189 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 257 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 126 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 100 optimal weight: 0.0020 chunk 63 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 48 GLN A 74 ASN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.155373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.123749 restraints weight = 12482.211| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.75 r_work: 0.3306 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11766 Z= 0.197 Angle : 0.577 6.568 16174 Z= 0.317 Chirality : 0.044 0.251 1823 Planarity : 0.004 0.041 1879 Dihedral : 18.974 179.251 2095 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.94 % Allowed : 16.32 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.23), residues: 1288 helix: 2.17 (0.20), residues: 608 sheet: -0.54 (0.35), residues: 207 loop : -0.55 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 21 TYR 0.015 0.002 TYR D 31 PHE 0.014 0.002 PHE F 263 TRP 0.009 0.001 TRP B 296 HIS 0.009 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (11766) covalent geometry : angle 0.57709 / 0.32 (16174) hydrogen bonds : bond 0.04876 / 3.35 ( 621) hydrogen bonds : angle 4.31798 / 3.09 ( 1724) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 174 time to evaluate : 0.241 Fit side-chains REVERT: A 58 MET cc_start: 0.9135 (ttp) cc_final: 0.8665 (ttp) REVERT: B 33 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.8131 (m-40) REVERT: B 302 LEU cc_start: 0.8285 (mt) cc_final: 0.8015 (mm) REVERT: C 17 ARG cc_start: 0.7948 (mtp85) cc_final: 0.7626 (mtm-85) REVERT: C 118 ARG cc_start: 0.7914 (ttt180) cc_final: 0.7699 (ttm-80) REVERT: D 3 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7853 (ttt) REVERT: D 23 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8594 (ptm) REVERT: E 31 LYS cc_start: 0.8154 (mtpm) cc_final: 0.7816 (mtpp) REVERT: E 33 ASN cc_start: 0.7801 (OUTLIER) cc_final: 0.7517 (m-40) REVERT: E 244 GLU cc_start: 0.7600 (tt0) cc_final: 0.7326 (tt0) REVERT: E 289 GLU cc_start: 0.6524 (OUTLIER) cc_final: 0.5541 (pp20) REVERT: E 291 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6850 (tt0) REVERT: F 72 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7729 (tt0) REVERT: F 138 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6146 (tt) REVERT: F 277 GLN cc_start: 0.8462 (tt0) cc_final: 0.8207 (tt0) outliers start: 42 outliers final: 23 residues processed: 196 average time/residue: 0.4675 time to fit residues: 99.3647 Evaluate side-chains 202 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 107 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 124 optimal weight: 0.3980 chunk 84 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.157720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.125997 restraints weight = 12403.720| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.79 r_work: 0.3337 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11766 Z= 0.140 Angle : 0.542 7.789 16174 Z= 0.298 Chirality : 0.042 0.258 1823 Planarity : 0.004 0.037 1879 Dihedral : 18.960 179.371 2095 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.28 % Allowed : 18.11 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.24), residues: 1288 helix: 2.27 (0.20), residues: 607 sheet: -0.41 (0.35), residues: 207 loop : -0.48 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 17 TYR 0.014 0.001 TYR F 223 PHE 0.010 0.001 PHE F 263 TRP 0.010 0.001 TRP B 296 HIS 0.005 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (11766) covalent geometry : angle 0.54177 / 0.30 (16174) hydrogen bonds : bond 0.04564 / 3.12 ( 621) hydrogen bonds : angle 4.25320 / 3.03 ( 1724) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 182 time to evaluate : 0.286 Fit side-chains REVERT: A 23 MET cc_start: 0.8848 (mtp) cc_final: 0.8562 (mtp) REVERT: A 58 MET cc_start: 0.9105 (ttp) cc_final: 0.8650 (ttp) REVERT: B 33 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.8143 (m-40) REVERT: B 124 ARG cc_start: 0.7934 (ttp-170) cc_final: 0.7733 (ttp-110) REVERT: B 172 ASN cc_start: 0.8736 (t0) cc_final: 0.8359 (t0) REVERT: B 302 LEU cc_start: 0.8204 (mt) cc_final: 0.7981 (mm) REVERT: C 17 ARG cc_start: 0.7882 (mtp85) cc_final: 0.7532 (mtm-85) REVERT: D 3 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7698 (ttt) REVERT: D 23 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8567 (ptm) REVERT: E 31 LYS cc_start: 0.8052 (mtpm) cc_final: 0.7613 (mttp) REVERT: E 33 ASN cc_start: 0.7768 (OUTLIER) cc_final: 0.7498 (m-40) REVERT: E 227 ASP cc_start: 0.8359 (m-30) cc_final: 0.8115 (m-30) REVERT: E 244 GLU cc_start: 0.7500 (tt0) cc_final: 0.7247 (tt0) REVERT: E 289 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.5418 (pp20) REVERT: F 72 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7649 (tt0) REVERT: F 277 GLN cc_start: 0.8403 (tt0) cc_final: 0.8148 (tt0) outliers start: 35 outliers final: 19 residues processed: 202 average time/residue: 0.4421 time to fit residues: 97.1232 Evaluate side-chains 189 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 87 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 0.1980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.155931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.123966 restraints weight = 12280.458| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.77 r_work: 0.3306 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11766 Z= 0.186 Angle : 0.580 7.337 16174 Z= 0.317 Chirality : 0.044 0.254 1823 Planarity : 0.004 0.034 1879 Dihedral : 18.942 179.068 2095 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.10 % Allowed : 18.95 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.23), residues: 1288 helix: 2.13 (0.20), residues: 607 sheet: -0.57 (0.35), residues: 212 loop : -0.52 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 124 TYR 0.017 0.002 TYR F 223 PHE 0.011 0.001 PHE F 263 TRP 0.010 0.001 TRP B 296 HIS 0.007 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (11766) covalent geometry : angle 0.58030 / 0.32 (16174) hydrogen bonds : bond 0.04754 / 3.27 ( 621) hydrogen bonds : angle 4.33765 / 3.10 ( 1724) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.250 Fit side-chains REVERT: A 23 MET cc_start: 0.8875 (mtp) cc_final: 0.8596 (mtp) REVERT: A 41 GLU cc_start: 0.7742 (tt0) cc_final: 0.7375 (tp30) REVERT: A 58 MET cc_start: 0.9126 (ttp) cc_final: 0.8654 (ttp) REVERT: B 124 ARG cc_start: 0.7910 (ttp-170) cc_final: 0.7707 (ttp-110) REVERT: B 172 ASN cc_start: 0.8753 (t0) cc_final: 0.8374 (t0) REVERT: B 302 LEU cc_start: 0.8247 (mt) cc_final: 0.7995 (mm) REVERT: C 17 ARG cc_start: 0.7888 (mtp85) cc_final: 0.7505 (mtm-85) REVERT: D 3 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7840 (ttt) REVERT: D 23 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8568 (ptm) REVERT: E 31 LYS cc_start: 0.8082 (mtpm) cc_final: 0.7749 (mtpp) REVERT: E 33 ASN cc_start: 0.7787 (OUTLIER) cc_final: 0.7498 (m-40) REVERT: E 244 GLU cc_start: 0.7509 (tt0) cc_final: 0.7238 (tt0) REVERT: E 289 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.5594 (pp20) REVERT: E 291 GLU cc_start: 0.7309 (mm-30) cc_final: 0.6782 (tt0) REVERT: F 72 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7660 (tt0) REVERT: F 277 GLN cc_start: 0.8411 (tt0) cc_final: 0.8145 (tt0) outliers start: 33 outliers final: 23 residues processed: 186 average time/residue: 0.4614 time to fit residues: 93.1501 Evaluate side-chains 200 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 66 optimal weight: 0.0030 chunk 56 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 88 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.157402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.125459 restraints weight = 12411.502| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.79 r_work: 0.3337 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11766 Z= 0.144 Angle : 0.563 7.609 16174 Z= 0.308 Chirality : 0.043 0.257 1823 Planarity : 0.004 0.043 1879 Dihedral : 18.930 179.094 2095 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.91 % Allowed : 19.23 % Favored : 77.86 % 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: 1.15 (0.24), residues: 1288 helix: 2.19 (0.20), residues: 607 sheet: -0.55 (0.35), residues: 212 loop : -0.45 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 124 TYR 0.018 0.001 TYR F 223 PHE 0.012 0.001 PHE F 263 TRP 0.010 0.001 TRP B 296 HIS 0.005 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (11766) covalent geometry : angle 0.56312 / 0.31 (16174) hydrogen bonds : bond 0.04540 / 3.11 ( 621) hydrogen bonds : angle 4.29053 / 3.06 ( 1724) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.281 Fit side-chains REVERT: A 23 MET cc_start: 0.8843 (mtp) cc_final: 0.8578 (mtp) REVERT: A 58 MET cc_start: 0.9100 (ttp) cc_final: 0.8638 (ttp) REVERT: B 33 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.8086 (m-40) REVERT: B 124 ARG cc_start: 0.7925 (ttp-170) cc_final: 0.7723 (ttp-110) REVERT: B 172 ASN cc_start: 0.8743 (t0) cc_final: 0.8366 (t0) REVERT: B 302 LEU cc_start: 0.8228 (mt) cc_final: 0.7996 (mm) REVERT: C 17 ARG cc_start: 0.7871 (mtp85) cc_final: 0.7501 (mtm-85) REVERT: C 263 PHE cc_start: 0.7880 (m-10) cc_final: 0.7619 (m-10) REVERT: D 3 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7706 (ttt) REVERT: D 23 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8530 (ptm) REVERT: E 31 LYS cc_start: 0.8004 (mtpm) cc_final: 0.7763 (mtpp) REVERT: E 33 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7492 (m-40) REVERT: E 227 ASP cc_start: 0.8368 (m-30) cc_final: 0.8137 (m-30) REVERT: E 244 GLU cc_start: 0.7496 (tt0) cc_final: 0.7293 (tt0) REVERT: E 289 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.5585 (pp20) REVERT: E 291 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6738 (tt0) REVERT: F 72 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7649 (tt0) REVERT: F 277 GLN cc_start: 0.8388 (tt0) cc_final: 0.8132 (tt0) outliers start: 31 outliers final: 23 residues processed: 194 average time/residue: 0.4429 time to fit residues: 93.9399 Evaluate side-chains 205 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 126 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 99 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN E 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.158361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.126551 restraints weight = 12421.896| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.78 r_work: 0.3341 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11766 Z= 0.136 Angle : 0.550 7.467 16174 Z= 0.301 Chirality : 0.042 0.258 1823 Planarity : 0.004 0.030 1879 Dihedral : 18.871 178.829 2095 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.19 % Allowed : 19.14 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.24), residues: 1288 helix: 2.22 (0.21), residues: 607 sheet: -0.35 (0.35), residues: 212 loop : -0.52 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 124 TYR 0.016 0.001 TYR F 223 PHE 0.008 0.001 PHE D 89 TRP 0.011 0.001 TRP B 296 HIS 0.005 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (11766) covalent geometry : angle 0.55034 / 0.30 (16174) hydrogen bonds : bond 0.04461 / 3.05 ( 621) hydrogen bonds : angle 4.23737 / 3.02 ( 1724) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3258.05 seconds wall clock time: 56 minutes 3.59 seconds (3363.59 seconds total)