Starting phenix.real_space_refine on Fri Jul 3 00:26:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fy9_29561/07_2026/8fy9_29561.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fy9_29561/07_2026/8fy9_29561.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fy9_29561/07_2026/8fy9_29561.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fy9_29561/07_2026/8fy9_29561.map" model { file = "/net/cci-nas-00/data/ceres_data/8fy9_29561/07_2026/8fy9_29561.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fy9_29561/07_2026/8fy9_29561.cif" } resolution = 3.1 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= 0.032 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 54 5.49 5 S 30 5.16 5 C 6628 2.51 5 N 1942 2.21 5 O 2088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10742 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: 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: "C" 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: "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: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 575 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Time building chain proxies: 2.26, per 1000 atoms: 0.21 Number of scatterers: 10742 At special positions: 0 Unit cell: (94.775, 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 30 16.00 P 54 15.00 O 2088 8.00 N 1942 7.00 C 6628 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: 1.04 Conformation dependent library (CDL) restraints added in 709.3 milliseconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 9 sheets defined 51.1% alpha, 14.8% beta 11 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 Processing helix chain 'A' and resid 36 through 51 Processing helix chain 'B' and resid 68 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: 4.070A 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 182 through 205 Processing helix chain 'B' and resid 219 through 230 removed outlier: 3.616A pdb=" N TYR B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 250 through 264 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: 3.729A 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 78 Processing helix chain 'C' and resid 102 through 114 removed outlier: 3.641A 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: 3.954A pdb=" N LEU C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 4.416A 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 Processing helix chain 'C' and resid 267 through 280 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 51 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 67 through 77 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 102 through 114 removed outlier: 3.922A pdb=" N ASN E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 182 through 205 Processing helix chain 'E' and resid 219 through 227 Processing helix chain 'E' and resid 233 through 245 Processing helix chain 'E' and resid 250 through 264 removed outlier: 3.945A pdb=" N LEU E 254 " --> pdb=" O ASP E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 280 removed outlier: 3.748A pdb=" N LEU E 280 " --> pdb=" O LEU E 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 21 removed outlier: 3.724A pdb=" N ARG F 21 " --> pdb=" O VAL F 18 " (cutoff:3.500A) 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 67 through 78 removed outlier: 3.868A pdb=" N VAL F 71 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 114 removed outlier: 3.760A 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: 4.476A pdb=" N LEU F 228 " --> pdb=" O ASP F 224 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR F 229 " --> pdb=" O VAL F 225 " (cutoff:3.500A) removed outlier: 4.097A 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: 3.745A 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: 5.291A pdb=" N GLU A 25 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL A 32 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 27 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N MET A 3 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA A 61 " --> pdb=" O MET A 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81 removed outlier: 5.277A pdb=" N ILE A 88 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 4.154A 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: 8.053A pdb=" N VAL B 57 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR B 23 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU B 59 " --> pdb=" O THR B 23 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE B 25 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU B 58 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 84 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU B 60 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TRP C 83 " --> pdb=" O ARG C 90 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N TYR C 92 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU C 81 " --> pdb=" O TYR C 92 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR C 23 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU C 59 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE C 25 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 39 through 41 removed outlier: 7.627A pdb=" N ALA B 30 " --> pdb=" O ASP B 65 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N SER B 67 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ILE B 32 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG C 34 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS C 31 " --> pdb=" O ALA C 42 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG C 49 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ILE D 88 " --> pdb=" O ARG C 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 49 removed outlier: 3.939A pdb=" N ASN B 308 " --> pdb=" O ARG B 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 24 through 27 removed outlier: 5.588A pdb=" N GLU D 25 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL D 32 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA D 27 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N MET D 3 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA D 61 " --> pdb=" O MET D 3 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 91 through 94 removed outlier: 6.563A pdb=" N TRP E 83 " --> pdb=" O TYR E 92 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER E 94 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU E 81 " --> pdb=" O SER E 94 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU E 58 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL E 84 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU E 60 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL E 57 " --> pdb=" O ARG E 21 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N THR E 23 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU E 59 " --> pdb=" O THR E 23 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE E 25 " --> pdb=" O LEU E 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 32 through 35 Processing sheet with id=AA9, first strand: chain 'F' and resid 22 through 27 removed outlier: 6.349A pdb=" N THR F 23 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LEU F 59 " --> pdb=" O THR F 23 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE F 25 " --> pdb=" O LEU F 59 " (cutoff:3.500A) 525 hydrogen bonds defined for protein. 1512 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 1.31 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: 3117 1.34 - 1.45: 1970 1.45 - 1.57: 5799 1.57 - 1.69: 108 1.69 - 1.81: 58 Bond restraints: 11052 Sorted by residual: bond pdb=" C3' DC G 6 " pdb=" C2' DC G 6 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DT G 12 " pdb=" C2' DT G 12 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DC G 8 " pdb=" C2' DC G 8 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.62e+00 bond pdb=" C3' DT H 20 " pdb=" C2' DT H 20 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.57e+00 bond pdb=" C3' DT G 16 " pdb=" C2' DT G 16 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.29e+00 ... (remaining 11047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 14945 1.98 - 3.96: 227 3.96 - 5.94: 18 5.94 - 7.92: 4 7.92 - 9.90: 2 Bond angle restraints: 15196 Sorted by residual: angle pdb=" CB ARG F 150 " pdb=" CG ARG F 150 " pdb=" CD ARG F 150 " ideal model delta sigma weight residual 111.30 121.20 -9.90 2.30e+00 1.89e-01 1.85e+01 angle pdb=" N3 DT G 16 " pdb=" C4 DT G 16 " pdb=" O4 DT G 16 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT G 9 " pdb=" C4 DT G 9 " pdb=" O4 DT G 9 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT H 20 " pdb=" C4 DT H 20 " pdb=" O4 DT H 20 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT H 9 " pdb=" C4 DT H 9 " pdb=" O4 DT H 9 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 ... (remaining 15191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.42: 6184 34.42 - 68.83: 314 68.83 - 103.25: 9 103.25 - 137.66: 0 137.66 - 172.08: 1 Dihedral angle restraints: 6508 sinusoidal: 2974 harmonic: 3534 Sorted by residual: 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 180.00 156.58 23.42 0 5.00e+00 4.00e-02 2.19e+01 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 220.00 47.92 172.08 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA ASP D 81 " pdb=" CB ASP D 81 " pdb=" CG ASP D 81 " pdb=" OD1 ASP D 81 " ideal model delta sinusoidal sigma weight residual -30.00 -89.67 59.67 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 6505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1371 0.050 - 0.100: 290 0.100 - 0.150: 63 0.150 - 0.199: 1 0.199 - 0.249: 1 Chirality restraints: 1726 Sorted by residual: chirality pdb=" CA ARG F 150 " pdb=" N ARG F 150 " pdb=" C ARG F 150 " pdb=" CB ARG F 150 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 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 -2.43 -0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CG LEU F 269 " pdb=" CB LEU F 269 " pdb=" CD1 LEU F 269 " pdb=" CD2 LEU F 269 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.38e-01 ... (remaining 1723 not shown) Planarity restraints: 1758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS E 190 " -0.010 2.00e-02 2.50e+03 1.45e-02 3.15e+00 pdb=" CG HIS E 190 " 0.030 2.00e-02 2.50e+03 pdb=" ND1 HIS E 190 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 HIS E 190 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 HIS E 190 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS E 190 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 143 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C LEU C 143 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU C 143 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG C 144 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 180 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.67e+00 pdb=" N PRO C 181 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 181 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 181 " 0.023 5.00e-02 4.00e+02 ... (remaining 1755 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1127 2.75 - 3.29: 10426 3.29 - 3.82: 19078 3.82 - 4.36: 22169 4.36 - 4.90: 38034 Nonbonded interactions: 90834 Sorted by model distance: nonbonded pdb=" O LEU E 295 " pdb=" OH TYR E 309 " model vdw 2.209 3.040 nonbonded pdb=" OH TYR C 229 " pdb=" OD2 ASP C 275 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR F 229 " pdb=" OD2 ASP F 275 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR F 126 " pdb=" NH2 ARG F 150 " model vdw 2.231 3.120 nonbonded pdb=" O LEU B 295 " pdb=" OH TYR B 309 " model vdw 2.238 3.040 ... (remaining 90829 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 129 or resid 181 through 283)) selection = (chain 'E' and resid 20 through 283) selection = (chain 'F' and (resid 20 through 129 or resid 181 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.020 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 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 0.034 11052 Z= 0.274 Angle : 0.566 9.896 15196 Z= 0.382 Chirality : 0.043 0.249 1726 Planarity : 0.004 0.049 1758 Dihedral : 17.515 172.077 4240 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.24), residues: 1212 helix: 2.00 (0.21), residues: 572 sheet: -0.19 (0.39), residues: 186 loop : -0.96 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 150 TYR 0.025 0.001 TYR B 126 PHE 0.010 0.001 PHE A 89 TRP 0.009 0.001 TRP A 44 HIS 0.019 0.002 HIS E 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.27 (11052) covalent geometry : angle 0.56633 / 0.38 (15196) hydrogen bonds : bond 0.15890 / 10.56 ( 553) hydrogen bonds : angle 6.28341 / 4.52 ( 1568) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.354 Fit side-chains REVERT: B 24 PHE cc_start: 0.6987 (m-10) cc_final: 0.6238 (m-10) REVERT: C 120 ARG cc_start: 0.7736 (ttp-110) cc_final: 0.7200 (ttp-110) REVERT: C 140 MET cc_start: 0.8612 (mpp) cc_final: 0.7969 (mpp) REVERT: D 57 SER cc_start: 0.8830 (p) cc_final: 0.8535 (p) REVERT: F 146 HIS cc_start: 0.6869 (m90) cc_final: 0.5941 (m90) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.1111 time to fit residues: 29.7506 Evaluate side-chains 166 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 146 HIS D 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.168017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.126703 restraints weight = 12498.250| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.23 r_work: 0.3441 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11052 Z= 0.179 Angle : 0.588 9.368 15196 Z= 0.328 Chirality : 0.044 0.256 1726 Planarity : 0.004 0.043 1758 Dihedral : 18.320 177.717 1978 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.50 % Allowed : 7.82 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.24), residues: 1212 helix: 1.89 (0.21), residues: 582 sheet: -0.27 (0.39), residues: 186 loop : -0.95 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 63 TYR 0.016 0.001 TYR F 126 PHE 0.016 0.001 PHE C 212 TRP 0.008 0.001 TRP E 83 HIS 0.015 0.002 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (11052) covalent geometry : angle 0.58785 / 0.33 (15196) hydrogen bonds : bond 0.04716 / 3.15 ( 553) hydrogen bonds : angle 4.64130 / 3.23 ( 1568) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: B 24 PHE cc_start: 0.7092 (m-10) cc_final: 0.6737 (m-10) REVERT: B 253 GLN cc_start: 0.8331 (tp40) cc_final: 0.8115 (tp40) REVERT: C 120 ARG cc_start: 0.7890 (ttp-110) cc_final: 0.7583 (ttp-110) REVERT: C 140 MET cc_start: 0.8740 (mpp) cc_final: 0.8039 (mpp) REVERT: D 9 LYS cc_start: 0.8140 (ptmm) cc_final: 0.7883 (ptmt) REVERT: D 82 TYR cc_start: 0.7876 (m-80) cc_final: 0.7562 (m-10) REVERT: E 115 GLU cc_start: 0.5249 (tp30) cc_final: 0.5023 (tp30) REVERT: F 128 MET cc_start: 0.8717 (mtp) cc_final: 0.8468 (mtp) REVERT: F 140 MET cc_start: 0.7742 (mmm) cc_final: 0.7453 (tpt) REVERT: F 250 ASP cc_start: 0.8362 (t0) cc_final: 0.7985 (t0) outliers start: 15 outliers final: 13 residues processed: 177 average time/residue: 0.1036 time to fit residues: 26.1219 Evaluate side-chains 178 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 265 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 3 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN B 29 HIS C 146 HIS D 48 GLN ** E 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.166214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.124766 restraints weight = 12614.046| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.23 r_work: 0.3399 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11052 Z= 0.200 Angle : 0.567 8.067 15196 Z= 0.313 Chirality : 0.043 0.225 1726 Planarity : 0.004 0.043 1758 Dihedral : 18.576 176.285 1978 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.00 % Allowed : 10.92 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.24), residues: 1212 helix: 1.87 (0.21), residues: 582 sheet: -0.13 (0.39), residues: 182 loop : -1.05 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 63 TYR 0.011 0.001 TYR F 223 PHE 0.011 0.001 PHE A 89 TRP 0.009 0.001 TRP E 83 HIS 0.012 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (11052) covalent geometry : angle 0.56657 / 0.31 (15196) hydrogen bonds : bond 0.04471 / 2.99 ( 553) hydrogen bonds : angle 4.45308 / 3.10 ( 1568) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.375 Fit side-chains REVERT: C 17 ARG cc_start: 0.7901 (mtm110) cc_final: 0.7681 (mtm110) REVERT: C 140 MET cc_start: 0.8678 (mpp) cc_final: 0.7998 (mpp) REVERT: D 1 MET cc_start: 0.6736 (mmt) cc_final: 0.6508 (mmm) REVERT: D 9 LYS cc_start: 0.8118 (ptmm) cc_final: 0.7832 (ptmt) REVERT: D 82 TYR cc_start: 0.7884 (m-80) cc_final: 0.7566 (m-80) REVERT: E 36 ASP cc_start: 0.7663 (p0) cc_final: 0.7381 (p0) REVERT: E 115 GLU cc_start: 0.5093 (tp30) cc_final: 0.4846 (tp30) REVERT: F 128 MET cc_start: 0.8771 (mtp) cc_final: 0.8466 (mtp) REVERT: F 140 MET cc_start: 0.7787 (mmm) cc_final: 0.7404 (tpt) REVERT: F 250 ASP cc_start: 0.8318 (t0) cc_final: 0.7939 (t0) outliers start: 20 outliers final: 19 residues processed: 177 average time/residue: 0.1018 time to fit residues: 25.7125 Evaluate side-chains 172 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 B residue 35 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 215 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 69 optimal weight: 0.9990 chunk 91 optimal weight: 0.1980 chunk 60 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 0.3980 chunk 100 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 29 HIS C 146 HIS D 48 GLN ** E 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.168107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.127156 restraints weight = 12570.389| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.24 r_work: 0.3432 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11052 Z= 0.137 Angle : 0.525 10.570 15196 Z= 0.293 Chirality : 0.041 0.235 1726 Planarity : 0.003 0.041 1758 Dihedral : 18.574 176.294 1978 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.30 % Allowed : 13.63 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.24), residues: 1212 helix: 1.99 (0.21), residues: 582 sheet: -0.13 (0.40), residues: 182 loop : -0.93 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 150 TYR 0.011 0.001 TYR F 126 PHE 0.012 0.001 PHE D 89 TRP 0.007 0.001 TRP D 44 HIS 0.008 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (11052) covalent geometry : angle 0.52496 / 0.29 (15196) hydrogen bonds : bond 0.03842 / 2.57 ( 553) hydrogen bonds : angle 4.31413 / 2.99 ( 1568) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.402 Fit side-chains REVERT: B 253 GLN cc_start: 0.8049 (tp40) cc_final: 0.7810 (tp40) REVERT: C 17 ARG cc_start: 0.7894 (mtm110) cc_final: 0.7655 (mtm110) REVERT: C 140 MET cc_start: 0.8533 (mpp) cc_final: 0.7969 (mpp) REVERT: D 9 LYS cc_start: 0.8073 (ptmm) cc_final: 0.7805 (ptmt) REVERT: D 82 TYR cc_start: 0.7817 (m-80) cc_final: 0.7540 (m-80) REVERT: E 227 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8196 (t70) REVERT: F 128 MET cc_start: 0.8700 (mtp) cc_final: 0.8432 (mtp) REVERT: F 140 MET cc_start: 0.7779 (mmm) cc_final: 0.7231 (tpp) outliers start: 23 outliers final: 16 residues processed: 177 average time/residue: 0.0883 time to fit residues: 22.4949 Evaluate side-chains 175 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 227 ASP Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 215 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 14 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 29 HIS D 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.165665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.124687 restraints weight = 12627.886| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.22 r_work: 0.3397 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11052 Z= 0.199 Angle : 0.564 7.656 15196 Z= 0.310 Chirality : 0.042 0.228 1726 Planarity : 0.004 0.041 1758 Dihedral : 18.674 175.256 1978 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.61 % Allowed : 14.83 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.24), residues: 1212 helix: 1.98 (0.21), residues: 582 sheet: -0.18 (0.40), residues: 182 loop : -1.00 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 256 TYR 0.011 0.001 TYR F 223 PHE 0.023 0.002 PHE F 176 TRP 0.008 0.001 TRP E 83 HIS 0.010 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (11052) covalent geometry : angle 0.56440 / 0.31 (15196) hydrogen bonds : bond 0.03995 / 2.67 ( 553) hydrogen bonds : angle 4.26966 / 2.97 ( 1568) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.243 Fit side-chains REVERT: C 17 ARG cc_start: 0.7943 (mtm110) cc_final: 0.7398 (mtp-110) REVERT: C 20 ASP cc_start: 0.8507 (m-30) cc_final: 0.7916 (m-30) REVERT: C 140 MET cc_start: 0.8834 (mpp) cc_final: 0.8117 (mpp) REVERT: C 246 GLU cc_start: 0.7144 (pm20) cc_final: 0.6320 (pp20) REVERT: D 9 LYS cc_start: 0.8108 (ptmm) cc_final: 0.7821 (ptmt) REVERT: E 115 GLU cc_start: 0.5116 (tp30) cc_final: 0.4835 (tp30) REVERT: E 227 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.8239 (t70) REVERT: F 128 MET cc_start: 0.8688 (mtp) cc_final: 0.8479 (mtp) REVERT: F 140 MET cc_start: 0.7751 (mmm) cc_final: 0.7184 (tpp) outliers start: 26 outliers final: 19 residues processed: 179 average time/residue: 0.0941 time to fit residues: 23.7895 Evaluate side-chains 181 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 227 ASP Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 215 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 117 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 51 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 42 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 29 HIS D 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.167873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.127047 restraints weight = 12566.543| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.24 r_work: 0.3430 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11052 Z= 0.139 Angle : 0.532 11.873 15196 Z= 0.294 Chirality : 0.041 0.232 1726 Planarity : 0.003 0.040 1758 Dihedral : 18.637 175.428 1978 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.20 % Allowed : 16.83 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.24), residues: 1212 helix: 2.07 (0.21), residues: 582 sheet: -0.14 (0.40), residues: 182 loop : -0.93 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 150 TYR 0.012 0.001 TYR C 223 PHE 0.015 0.001 PHE F 176 TRP 0.007 0.001 TRP E 83 HIS 0.007 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (11052) covalent geometry : angle 0.53203 / 0.29 (15196) hydrogen bonds : bond 0.03649 / 2.45 ( 553) hydrogen bonds : angle 4.19609 / 2.92 ( 1568) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.257 Fit side-chains REVERT: C 17 ARG cc_start: 0.7916 (mtm110) cc_final: 0.7662 (mtm110) REVERT: C 140 MET cc_start: 0.8739 (mpp) cc_final: 0.8072 (mpp) REVERT: D 9 LYS cc_start: 0.8068 (ptmm) cc_final: 0.7806 (ptmt) REVERT: E 66 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7978 (tp) REVERT: E 227 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8222 (t70) REVERT: F 140 MET cc_start: 0.7731 (mmm) cc_final: 0.7163 (tpp) outliers start: 22 outliers final: 16 residues processed: 183 average time/residue: 0.0880 time to fit residues: 23.0630 Evaluate side-chains 172 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 227 ASP Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 215 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 117 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 110 optimal weight: 0.0770 chunk 99 optimal weight: 0.7980 chunk 103 optimal weight: 10.0000 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 29 HIS D 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.168383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.127518 restraints weight = 12506.211| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.25 r_work: 0.3449 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11052 Z= 0.135 Angle : 0.527 7.504 15196 Z= 0.291 Chirality : 0.041 0.231 1726 Planarity : 0.003 0.040 1758 Dihedral : 18.615 175.172 1978 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.51 % Allowed : 17.03 % Favored : 80.46 % 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: 1.00 (0.24), residues: 1212 helix: 2.08 (0.21), residues: 582 sheet: -0.14 (0.39), residues: 182 loop : -0.91 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 120 TYR 0.011 0.001 TYR F 126 PHE 0.012 0.001 PHE D 89 TRP 0.006 0.001 TRP E 83 HIS 0.008 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (11052) covalent geometry : angle 0.52656 / 0.29 (15196) hydrogen bonds : bond 0.03569 / 2.40 ( 553) hydrogen bonds : angle 4.17004 / 2.90 ( 1568) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.256 Fit side-chains REVERT: C 17 ARG cc_start: 0.8002 (mtm110) cc_final: 0.7740 (mtm110) REVERT: C 140 MET cc_start: 0.8731 (mpp) cc_final: 0.8092 (mpp) REVERT: D 9 LYS cc_start: 0.8089 (ptmm) cc_final: 0.7834 (ptmt) REVERT: E 125 MET cc_start: 0.7639 (tpp) cc_final: 0.7349 (mmt) REVERT: E 227 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8231 (t70) REVERT: F 140 MET cc_start: 0.7691 (mmm) cc_final: 0.7094 (tpp) outliers start: 25 outliers final: 16 residues processed: 172 average time/residue: 0.0874 time to fit residues: 21.6303 Evaluate side-chains 167 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 227 ASP Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 215 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 3 optimal weight: 3.9990 chunk 121 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 95 optimal weight: 0.0980 chunk 124 optimal weight: 8.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 29 HIS D 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.167693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.126919 restraints weight = 12581.353| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.24 r_work: 0.3425 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11052 Z= 0.151 Angle : 0.546 13.702 15196 Z= 0.297 Chirality : 0.042 0.229 1726 Planarity : 0.003 0.039 1758 Dihedral : 18.631 174.978 1978 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.30 % Allowed : 16.73 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.24), residues: 1212 helix: 2.08 (0.21), residues: 582 sheet: -0.14 (0.39), residues: 182 loop : -0.94 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 150 TYR 0.013 0.001 TYR F 126 PHE 0.011 0.001 PHE D 89 TRP 0.007 0.001 TRP E 83 HIS 0.007 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (11052) covalent geometry : angle 0.54552 / 0.30 (15196) hydrogen bonds : bond 0.03603 / 2.42 ( 553) hydrogen bonds : angle 4.15341 / 2.89 ( 1568) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.388 Fit side-chains REVERT: C 17 ARG cc_start: 0.7992 (mtm110) cc_final: 0.7641 (mtp-110) REVERT: C 140 MET cc_start: 0.8629 (mpp) cc_final: 0.7985 (mpp) REVERT: C 246 GLU cc_start: 0.7000 (pm20) cc_final: 0.6106 (pp20) REVERT: D 9 LYS cc_start: 0.8086 (ptmm) cc_final: 0.7817 (ptmt) REVERT: E 227 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8255 (t70) REVERT: F 140 MET cc_start: 0.7707 (mmm) cc_final: 0.7125 (tpp) outliers start: 23 outliers final: 17 residues processed: 171 average time/residue: 0.1014 time to fit residues: 24.6019 Evaluate side-chains 168 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 227 ASP Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 215 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 117 optimal weight: 0.0980 chunk 13 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 99 optimal weight: 0.0980 chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 29 HIS D 48 GLN E 190 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.169775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.131079 restraints weight = 12453.359| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.17 r_work: 0.3467 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11052 Z= 0.120 Angle : 0.511 7.620 15196 Z= 0.282 Chirality : 0.041 0.232 1726 Planarity : 0.003 0.039 1758 Dihedral : 18.554 174.964 1978 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.00 % Allowed : 17.54 % Favored : 80.46 % 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: 1212 helix: 2.14 (0.21), residues: 582 sheet: -0.10 (0.39), residues: 182 loop : -0.92 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 120 TYR 0.015 0.001 TYR F 126 PHE 0.012 0.001 PHE D 89 TRP 0.007 0.001 TRP D 44 HIS 0.005 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (11052) covalent geometry : angle 0.51138 / 0.28 (15196) hydrogen bonds : bond 0.03367 / 2.25 ( 553) hydrogen bonds : angle 4.10790 / 2.85 ( 1568) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.324 Fit side-chains REVERT: C 17 ARG cc_start: 0.8001 (mtm110) cc_final: 0.7692 (mtm110) REVERT: C 140 MET cc_start: 0.8591 (mpp) cc_final: 0.7982 (mpp) REVERT: D 9 LYS cc_start: 0.8095 (ptmm) cc_final: 0.7807 (ptmt) REVERT: F 140 MET cc_start: 0.7656 (mmm) cc_final: 0.7059 (tpp) REVERT: F 150 ARG cc_start: 0.7854 (ptp90) cc_final: 0.7590 (ptp90) outliers start: 20 outliers final: 14 residues processed: 173 average time/residue: 0.1011 time to fit residues: 24.8330 Evaluate side-chains 170 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 91 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 120 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 0.0770 chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 29 HIS D 48 GLN E 190 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.168359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.127848 restraints weight = 12466.217| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.23 r_work: 0.3438 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11052 Z= 0.145 Angle : 0.539 13.777 15196 Z= 0.293 Chirality : 0.041 0.229 1726 Planarity : 0.003 0.038 1758 Dihedral : 18.612 174.624 1978 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.70 % Allowed : 18.14 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.24), residues: 1212 helix: 2.13 (0.21), residues: 582 sheet: -0.13 (0.39), residues: 182 loop : -0.94 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 77 TYR 0.013 0.001 TYR F 126 PHE 0.011 0.001 PHE C 212 TRP 0.006 0.001 TRP E 83 HIS 0.007 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (11052) covalent geometry : angle 0.53896 / 0.29 (15196) hydrogen bonds : bond 0.03491 / 2.34 ( 553) hydrogen bonds : angle 4.11590 / 2.85 ( 1568) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.382 Fit side-chains REVERT: B 272 MET cc_start: 0.7363 (ttm) cc_final: 0.7142 (mtt) REVERT: C 17 ARG cc_start: 0.7972 (mtm110) cc_final: 0.7618 (mtp-110) REVERT: C 140 MET cc_start: 0.8616 (mpp) cc_final: 0.7984 (mpp) REVERT: D 9 LYS cc_start: 0.8087 (ptmm) cc_final: 0.7809 (ptmt) REVERT: F 140 MET cc_start: 0.7691 (mmm) cc_final: 0.7114 (tpp) REVERT: F 146 HIS cc_start: 0.6515 (m90) cc_final: 0.6285 (m90) REVERT: F 150 ARG cc_start: 0.7821 (ptp90) cc_final: 0.7539 (ptp90) REVERT: F 250 ASP cc_start: 0.8342 (t0) cc_final: 0.7894 (t0) outliers start: 17 outliers final: 14 residues processed: 171 average time/residue: 0.0958 time to fit residues: 23.5966 Evaluate side-chains 164 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 81 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 29 HIS D 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.168099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.127520 restraints weight = 12547.276| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.23 r_work: 0.3435 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11052 Z= 0.148 Angle : 0.543 13.713 15196 Z= 0.293 Chirality : 0.042 0.229 1726 Planarity : 0.003 0.038 1758 Dihedral : 18.659 174.699 1978 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.90 % Allowed : 17.33 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.24), residues: 1212 helix: 2.12 (0.21), residues: 582 sheet: -0.12 (0.40), residues: 172 loop : -0.97 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 120 TYR 0.016 0.001 TYR F 126 PHE 0.011 0.001 PHE C 212 TRP 0.007 0.001 TRP E 83 HIS 0.007 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (11052) covalent geometry : angle 0.54301 / 0.29 (15196) hydrogen bonds : bond 0.03502 / 2.36 ( 553) hydrogen bonds : angle 4.12143 / 2.86 ( 1568) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2272.10 seconds wall clock time: 39 minutes 42.02 seconds (2382.02 seconds total)