Starting phenix.real_space_refine on Fri Jul 3 10:52:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fyb_29563/07_2026/8fyb_29563.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fyb_29563/07_2026/8fyb_29563.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 { model { file = "/net/cci-nas-00/data/ceres_data/8fyb_29563/07_2026/8fyb_29563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fyb_29563/07_2026/8fyb_29563.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fyb_29563/07_2026/8fyb_29563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fyb_29563/07_2026/8fyb_29563.map" } 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= 0.031 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 571 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 135 5.49 5 S 32 5.16 5 C 8099 2.51 5 N 2441 2.21 5 O 2779 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: 13486 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 737 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} 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: 2414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2414 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 13, 'TRANS': 295} 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: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2295 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain: "F" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2188 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 10, 'TRANS': 270} Chain: "G" Number of atoms: 1089 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 52, 1067 Classifications: {'DNA': 52} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 51} Conformer: "B" Number of residues, atoms: 52, 1067 Classifications: {'DNA': 52} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 51} bond proxies already assigned to first conformer: 1170 Chain: "H" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 632 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Chain: "J" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 742 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "I" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 348 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A DG G 29 " occ=0.50 ... (42 atoms not shown) pdb=" C4 B DG G 29 " occ=0.50 Time building chain proxies: 2.83, per 1000 atoms: 0.21 Number of scatterers: 13486 At special positions: 0 Unit cell: (123.765, 97.005, 163.905, 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 32 16.00 P 135 15.00 O 2779 8.00 N 2441 7.00 C 8099 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: 0.84 Conformation dependent library (CDL) restraints added in 517.4 milliseconds 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2510 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 11 sheets defined 51.5% alpha, 14.4% beta 33 base pairs and 109 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 Processing helix chain 'A' and resid 36 through 50 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: 3.838A pdb=" N ASN B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 130 Processing helix chain 'B' and resid 139 through 162 Processing helix chain 'B' and resid 180 through 205 removed outlier: 3.591A pdb=" N LEU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 231 removed outlier: 4.028A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 4.648A 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 263 removed outlier: 3.535A pdb=" N LEU B 254 " --> pdb=" O ASP B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 280 Processing helix chain 'B' and resid 283 through 287 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: 4.084A 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 removed outlier: 3.643A pdb=" N THR C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 114 removed outlier: 3.830A pdb=" N LYS C 107 " --> pdb=" O ARG C 103 " (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 204 removed outlier: 3.799A pdb=" N ALA C 192 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 231 removed outlier: 3.687A pdb=" N LEU C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TYR C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 4.330A 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 removed outlier: 3.688A 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 51 Processing helix chain 'E' and resid 51 through 55 removed outlier: 3.790A pdb=" N MET E 54 " --> pdb=" O PRO E 51 " (cutoff:3.500A) 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: 4.379A pdb=" N ASN E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 130 Processing helix chain 'E' and resid 139 through 162 Processing helix chain 'E' and resid 180 through 205 Processing helix chain 'E' and resid 219 through 231 removed outlier: 4.771A pdb=" N LEU E 228 " --> pdb=" O ASP E 224 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TYR E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA E 231 " --> pdb=" O ASP E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 244 Processing helix chain 'E' and resid 250 through 266 removed outlier: 4.022A pdb=" N LEU E 254 " --> pdb=" O ASP E 250 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY E 266 " --> pdb=" O ALA E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 280 removed outlier: 3.854A pdb=" N LYS E 270 " --> pdb=" O GLY E 266 " (cutoff:3.500A) removed outlier: 3.531A 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 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' 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 77 removed outlier: 3.703A pdb=" N VAL F 71 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 114 removed outlier: 3.635A 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 removed outlier: 3.681A pdb=" N ALA F 192 " --> pdb=" O ALA F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 244 removed outlier: 3.767A pdb=" N TYR F 229 " --> pdb=" O VAL F 225 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ALA F 231 " --> pdb=" O ASP F 227 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N GLU F 232 " --> pdb=" O LEU F 228 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL F 235 " --> pdb=" O ALA F 231 " (cutoff:3.500A) Proline residue: F 236 - end of helix Processing helix chain 'F' and resid 250 through 267 Processing helix chain 'F' and resid 267 through 280 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 5.939A pdb=" N GLU A 25 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL A 32 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N MET A 3 " --> pdb=" O ALA A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81 removed outlier: 5.717A pdb=" N ILE A 88 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARG F 49 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA E 30 " --> pdb=" O ASP E 65 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER E 67 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ILE E 32 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 91 through 94 removed outlier: 6.608A pdb=" N TRP B 83 " --> pdb=" O TYR B 92 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N SER B 94 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL B 57 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N THR B 23 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU B 59 " --> pdb=" O THR B 23 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE B 25 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA B 22 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 39 through 40 removed outlier: 6.988A pdb=" N ALA B 30 " --> pdb=" O ASP B 65 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N SER B 67 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE B 32 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG C 34 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG C 49 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 5.518A 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 48 Processing sheet with id=AA6, first strand: chain 'B' and resid 214 through 215 Processing sheet with id=AA7, first strand: chain 'C' and resid 22 through 27 removed outlier: 6.395A pdb=" N THR C 23 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU C 59 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE C 25 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA C 80 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR C 91 " --> pdb=" O TRP C 83 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLY C 85 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N VAL C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 24 through 27 removed outlier: 5.806A pdb=" N GLU D 25 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL D 32 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA D 27 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET D 3 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA D 61 " --> pdb=" O MET D 3 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 91 through 94 removed outlier: 6.049A pdb=" N LEU E 58 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL E 84 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU E 60 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL E 57 " --> pdb=" O ARG E 21 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THR E 23 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU E 59 " --> pdb=" O THR E 23 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE E 25 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR E 26 " --> pdb=" O LEU E 293 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 47 through 49 removed outlier: 4.078A pdb=" N ASN E 308 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 22 through 27 removed outlier: 6.463A pdb=" N THR F 23 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU F 59 " --> pdb=" O THR F 23 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE F 25 " --> pdb=" O LEU F 59 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL F 82 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR F 91 " --> pdb=" O TRP F 83 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLY F 85 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL F 89 " --> pdb=" O GLY F 85 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1656 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 110 stacking parallelities Total time for adding SS restraints: 2.25 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3437 1.33 - 1.45: 3290 1.45 - 1.57: 6968 1.57 - 1.69: 269 1.69 - 1.82: 62 Bond restraints: 14026 Sorted by residual: bond pdb=" C3' DT I 40 " pdb=" C2' DT I 40 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.27e+01 bond pdb=" C3' DG G 38 " pdb=" C2' DG G 38 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C3' DT G 30 " pdb=" C2' DT G 30 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DA I 31 " pdb=" C2' DA I 31 " 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 39 " pdb=" C2' DC G 39 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 14021 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 18945 1.82 - 3.64: 583 3.64 - 5.47: 37 5.47 - 7.29: 6 7.29 - 9.11: 2 Bond angle restraints: 19573 Sorted by residual: angle pdb=" N LYS E 167 " pdb=" CA LYS E 167 " pdb=" C LYS E 167 " ideal model delta sigma weight residual 110.53 102.86 7.67 1.29e+00 6.01e-01 3.54e+01 angle pdb=" N LYS E 168 " pdb=" CA LYS E 168 " pdb=" C LYS E 168 " ideal model delta sigma weight residual 110.35 117.00 -6.65 1.36e+00 5.41e-01 2.39e+01 angle pdb=" N TRP E 166 " pdb=" CA TRP E 166 " pdb=" C TRP E 166 " ideal model delta sigma weight residual 107.37 116.48 -9.11 2.07e+00 2.33e-01 1.94e+01 angle pdb=" N3 DT G 21 " pdb=" C4 DT G 21 " pdb=" O4 DT G 21 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT I 36 " pdb=" C4 DT I 36 " pdb=" O4 DT I 36 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 ... (remaining 19568 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 7454 35.90 - 71.81: 584 71.81 - 107.71: 17 107.71 - 143.62: 3 143.62 - 179.52: 4 Dihedral angle restraints: 8062 sinusoidal: 4145 harmonic: 3917 Sorted by residual: dihedral pdb=" C4' DA J 30 " pdb=" C3' DA J 30 " pdb=" O3' DA J 30 " pdb=" P DA J 31 " ideal model delta sinusoidal sigma weight residual -140.00 39.52 -179.52 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 25 " pdb=" C3' DG J 25 " pdb=" O3' DG J 25 " pdb=" P DC J 26 " ideal model delta sinusoidal sigma weight residual 220.00 41.59 178.41 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA J 31 " pdb=" C3' DA J 31 " pdb=" O3' DA J 31 " pdb=" P DA J 32 " ideal model delta sinusoidal sigma weight residual -140.00 38.10 -178.10 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 8059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1477 0.039 - 0.079: 501 0.079 - 0.118: 176 0.118 - 0.157: 39 0.157 - 0.196: 2 Chirality restraints: 2195 Sorted by residual: chirality pdb=" CA LYS E 168 " pdb=" N LYS E 168 " pdb=" C LYS E 168 " pdb=" CB LYS E 168 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.64e-01 chirality pdb=" CA TRP E 166 " pdb=" N TRP E 166 " pdb=" C TRP E 166 " pdb=" CB TRP E 166 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.65e-01 chirality pdb=" CA VAL B 303 " pdb=" N VAL B 303 " pdb=" C VAL B 303 " pdb=" CB VAL B 303 " both_signs ideal model delta sigma weight residual False 2.44 2.29 0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 2192 not shown) Planarity restraints: 2042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 50 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.80e+00 pdb=" N PRO B 51 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 51 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 51 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 291 " -0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO E 292 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO E 292 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 292 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 160 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C LYS E 160 " -0.029 2.00e-02 2.50e+03 pdb=" O LYS E 160 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS E 161 " 0.010 2.00e-02 2.50e+03 ... (remaining 2039 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1663 2.75 - 3.29: 12870 3.29 - 3.82: 25087 3.82 - 4.36: 29445 4.36 - 4.90: 47320 Nonbonded interactions: 116385 Sorted by model distance: nonbonded pdb=" OH TYR E 223 " pdb=" N2 DG G 27 " model vdw 2.211 3.120 nonbonded pdb=" NH2 ARG E 124 " pdb=" OE1 GLU E 281 " model vdw 2.248 3.120 nonbonded pdb=" OH TYR B 126 " pdb=" O4 DT H 29 " model vdw 2.253 3.040 nonbonded pdb=" NH2 ARG B 256 " pdb=" OP1 DT H 23 " model vdw 2.254 3.120 nonbonded pdb=" OH TYR E 92 " pdb=" OP2 DC G 24 " model vdw 2.254 3.040 ... (remaining 116380 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' and resid 1 through 92) } ncs_group { reference = (chain 'B' and resid 20 through 282) selection = (chain 'C' and resid 20 through 282) selection = (chain 'E' and resid 20 through 282) selection = (chain 'F' and resid 20 through 282) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.550 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14026 Z= 0.386 Angle : 0.672 9.109 19573 Z= 0.506 Chirality : 0.045 0.196 2195 Planarity : 0.004 0.049 2042 Dihedral : 20.880 179.521 5552 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.09 % Allowed : 0.18 % Favored : 99.73 % 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: 0.63 (0.23), residues: 1347 helix: 1.66 (0.20), residues: 635 sheet: -0.29 (0.37), residues: 214 loop : -0.85 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 116 TYR 0.015 0.002 TYR E 162 PHE 0.017 0.002 PHE A 35 TRP 0.013 0.001 TRP E 166 HIS 0.012 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.39 (14026) covalent geometry : angle 0.67164 / 0.51 (19573) hydrogen bonds : bond 0.14203 / 9.74 ( 655) hydrogen bonds : angle 6.27044 / 4.36 ( 1812) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 294 time to evaluate : 0.277 Fit side-chains REVERT: A 3 MET cc_start: 0.7611 (ttt) cc_final: 0.6837 (ttt) REVERT: B 175 ASP cc_start: 0.7927 (t0) cc_final: 0.7550 (t70) REVERT: B 275 ASP cc_start: 0.7542 (m-30) cc_final: 0.7199 (m-30) REVERT: B 289 GLU cc_start: 0.7826 (tp30) cc_final: 0.7613 (tp30) REVERT: C 162 TYR cc_start: 0.8341 (m-80) cc_final: 0.7963 (m-80) REVERT: C 233 ILE cc_start: 0.7577 (mt) cc_final: 0.7260 (mt) REVERT: C 274 LYS cc_start: 0.8113 (tppt) cc_final: 0.7883 (tptp) REVERT: E 72 GLU cc_start: 0.7249 (tp30) cc_final: 0.6892 (mm-30) REVERT: E 76 ASP cc_start: 0.6861 (m-30) cc_final: 0.6636 (m-30) REVERT: E 154 LYS cc_start: 0.7294 (tppp) cc_final: 0.6566 (tppt) REVERT: E 172 ASN cc_start: 0.8074 (t0) cc_final: 0.7646 (t0) REVERT: E 175 ASP cc_start: 0.7559 (t70) cc_final: 0.7091 (m-30) REVERT: E 193 LEU cc_start: 0.8391 (tp) cc_final: 0.8148 (tp) REVERT: E 272 MET cc_start: 0.7782 (mtt) cc_final: 0.7550 (mtp) REVERT: F 101 SER cc_start: 0.8939 (t) cc_final: 0.8702 (p) REVERT: F 275 ASP cc_start: 0.8134 (m-30) cc_final: 0.7843 (m-30) outliers start: 1 outliers final: 0 residues processed: 295 average time/residue: 0.1228 time to fit residues: 49.9130 Evaluate side-chains 186 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 33 ASN E 183 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 = 0.4192 r_free = 0.4192 target = 0.178159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.112561 restraints weight = 15611.907| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.21 r_work: 0.3265 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14026 Z= 0.245 Angle : 0.686 6.703 19573 Z= 0.389 Chirality : 0.048 0.251 2195 Planarity : 0.005 0.048 2042 Dihedral : 24.193 178.291 3008 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.44 % Allowed : 9.44 % Favored : 89.12 % 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: 0.47 (0.22), residues: 1347 helix: 1.56 (0.20), residues: 641 sheet: -0.45 (0.36), residues: 212 loop : -0.96 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 49 TYR 0.017 0.002 TYR B 92 PHE 0.013 0.002 PHE C 24 TRP 0.015 0.002 TRP C 296 HIS 0.010 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.24 (14026) covalent geometry : angle 0.68608 / 0.39 (19573) hydrogen bonds : bond 0.05424 / 3.64 ( 655) hydrogen bonds : angle 4.47895 / 3.18 ( 1812) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 200 time to evaluate : 0.295 Fit side-chains REVERT: A 3 MET cc_start: 0.8232 (ttt) cc_final: 0.7704 (ttt) REVERT: A 45 ARG cc_start: 0.7643 (mmm-85) cc_final: 0.7338 (mtp85) REVERT: A 73 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7947 (tp30) REVERT: B 138 LEU cc_start: 0.8658 (mp) cc_final: 0.8371 (tp) REVERT: B 175 ASP cc_start: 0.8121 (t0) cc_final: 0.7912 (t0) REVERT: B 281 GLU cc_start: 0.8053 (mp0) cc_final: 0.7733 (mp0) REVERT: B 289 GLU cc_start: 0.8257 (tp30) cc_final: 0.7820 (tp30) REVERT: C 156 ARG cc_start: 0.7628 (mtm110) cc_final: 0.7300 (ptt90) REVERT: C 162 TYR cc_start: 0.8297 (m-80) cc_final: 0.8024 (m-80) REVERT: C 274 LYS cc_start: 0.8291 (tppt) cc_final: 0.8072 (tptp) REVERT: D 78 SER cc_start: 0.8261 (m) cc_final: 0.7939 (t) REVERT: E 72 GLU cc_start: 0.7838 (tp30) cc_final: 0.6862 (tp30) REVERT: E 76 ASP cc_start: 0.7296 (m-30) cc_final: 0.6811 (m-30) REVERT: E 140 MET cc_start: 0.6459 (mmt) cc_final: 0.6101 (mmt) REVERT: E 172 ASN cc_start: 0.7860 (t0) cc_final: 0.7500 (t0) REVERT: F 101 SER cc_start: 0.9213 (t) cc_final: 0.8858 (p) REVERT: F 275 ASP cc_start: 0.8338 (m-30) cc_final: 0.8032 (m-30) outliers start: 16 outliers final: 11 residues processed: 210 average time/residue: 0.1165 time to fit residues: 34.9532 Evaluate side-chains 196 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 185 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 237 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 41 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 105 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 183 ASN E 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.180707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.118265 restraints weight = 16839.036| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.40 r_work: 0.3270 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14026 Z= 0.153 Angle : 0.586 6.498 19573 Z= 0.338 Chirality : 0.044 0.285 2195 Planarity : 0.004 0.052 2042 Dihedral : 24.414 173.532 3008 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.17 % Allowed : 12.05 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.23), residues: 1347 helix: 1.76 (0.20), residues: 641 sheet: -0.49 (0.36), residues: 214 loop : -0.84 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 116 TYR 0.023 0.001 TYR F 126 PHE 0.011 0.001 PHE A 89 TRP 0.008 0.001 TRP C 296 HIS 0.007 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (14026) covalent geometry : angle 0.58571 / 0.34 (19573) hydrogen bonds : bond 0.04445 / 2.96 ( 655) hydrogen bonds : angle 4.15436 / 2.96 ( 1812) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 200 time to evaluate : 0.297 Fit side-chains REVERT: A 3 MET cc_start: 0.7869 (ttt) cc_final: 0.7085 (ttt) REVERT: A 45 ARG cc_start: 0.7463 (mmm-85) cc_final: 0.7130 (mtp85) REVERT: A 73 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7542 (tp30) REVERT: B 175 ASP cc_start: 0.8017 (t0) cc_final: 0.7807 (t0) REVERT: B 289 GLU cc_start: 0.8132 (tp30) cc_final: 0.7637 (tp30) REVERT: C 150 ARG cc_start: 0.7021 (mmt90) cc_final: 0.6765 (mtt90) REVERT: C 156 ARG cc_start: 0.7511 (mtm110) cc_final: 0.7171 (ptt90) REVERT: C 162 TYR cc_start: 0.8241 (m-80) cc_final: 0.7876 (m-80) REVERT: C 253 GLN cc_start: 0.7841 (mt0) cc_final: 0.7483 (mm-40) REVERT: C 300 GLU cc_start: 0.7995 (tp30) cc_final: 0.7793 (tp30) REVERT: D 78 SER cc_start: 0.8176 (m) cc_final: 0.7812 (t) REVERT: E 72 GLU cc_start: 0.7583 (tp30) cc_final: 0.6664 (tm-30) REVERT: E 76 ASP cc_start: 0.7134 (m-30) cc_final: 0.6454 (m-30) REVERT: E 155 TYR cc_start: 0.7220 (m-10) cc_final: 0.6910 (m-80) REVERT: E 172 ASN cc_start: 0.7937 (t0) cc_final: 0.7540 (t0) REVERT: E 193 LEU cc_start: 0.8412 (tp) cc_final: 0.8171 (tp) REVERT: F 101 SER cc_start: 0.9162 (t) cc_final: 0.8791 (p) outliers start: 13 outliers final: 8 residues processed: 209 average time/residue: 0.1184 time to fit residues: 35.2488 Evaluate side-chains 183 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 175 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 277 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 124 optimal weight: 10.0000 chunk 113 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 129 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 123 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.180430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.118097 restraints weight = 18613.356| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.41 r_work: 0.3262 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14026 Z= 0.151 Angle : 0.581 6.436 19573 Z= 0.335 Chirality : 0.043 0.245 2195 Planarity : 0.004 0.051 2042 Dihedral : 24.456 172.666 3008 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.71 % Allowed : 12.86 % Favored : 85.43 % 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: 0.74 (0.23), residues: 1347 helix: 1.84 (0.20), residues: 641 sheet: -0.45 (0.36), residues: 214 loop : -0.87 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 116 TYR 0.017 0.001 TYR F 126 PHE 0.011 0.001 PHE A 89 TRP 0.011 0.001 TRP C 296 HIS 0.006 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (14026) covalent geometry : angle 0.58071 / 0.34 (19573) hydrogen bonds : bond 0.04166 / 2.77 ( 655) hydrogen bonds : angle 4.00670 / 2.85 ( 1812) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7566 (mmm-85) cc_final: 0.7206 (mtp85) REVERT: A 73 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7603 (tp30) REVERT: B 138 LEU cc_start: 0.8178 (tp) cc_final: 0.7965 (tp) REVERT: B 175 ASP cc_start: 0.8073 (t0) cc_final: 0.7860 (t0) REVERT: C 253 GLN cc_start: 0.7805 (mt0) cc_final: 0.7409 (mm-40) REVERT: D 55 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8178 (mt-10) REVERT: D 78 SER cc_start: 0.8195 (m) cc_final: 0.7834 (t) REVERT: E 72 GLU cc_start: 0.7603 (tp30) cc_final: 0.6690 (tm-30) REVERT: E 76 ASP cc_start: 0.7155 (m-30) cc_final: 0.6472 (m-30) REVERT: E 172 ASN cc_start: 0.7998 (t0) cc_final: 0.7632 (t0) REVERT: E 193 LEU cc_start: 0.8425 (tp) cc_final: 0.8191 (tp) REVERT: F 101 SER cc_start: 0.9143 (t) cc_final: 0.8739 (p) outliers start: 19 outliers final: 16 residues processed: 193 average time/residue: 0.1013 time to fit residues: 28.0978 Evaluate side-chains 188 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 277 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 76 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 116 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 109 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.179445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.116792 restraints weight = 16033.571| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.28 r_work: 0.3264 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14026 Z= 0.163 Angle : 0.573 6.277 19573 Z= 0.331 Chirality : 0.043 0.248 2195 Planarity : 0.004 0.051 2042 Dihedral : 24.516 172.278 3008 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.25 % Allowed : 13.58 % Favored : 84.17 % 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: 0.74 (0.23), residues: 1347 helix: 1.90 (0.20), residues: 640 sheet: -0.53 (0.36), residues: 210 loop : -0.91 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 116 TYR 0.015 0.001 TYR F 126 PHE 0.011 0.001 PHE D 89 TRP 0.007 0.001 TRP B 83 HIS 0.007 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (14026) covalent geometry : angle 0.57270 / 0.33 (19573) hydrogen bonds : bond 0.04162 / 2.80 ( 655) hydrogen bonds : angle 3.92262 / 2.80 ( 1812) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.346 Fit side-chains REVERT: A 3 MET cc_start: 0.8092 (ttt) cc_final: 0.7432 (ttt) REVERT: A 45 ARG cc_start: 0.7828 (mmm-85) cc_final: 0.7500 (mtp85) REVERT: A 73 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7910 (tp30) REVERT: B 116 ARG cc_start: 0.8610 (mmm-85) cc_final: 0.8402 (mmp80) REVERT: B 175 ASP cc_start: 0.8160 (t0) cc_final: 0.7947 (t0) REVERT: C 128 MET cc_start: 0.7806 (mtm) cc_final: 0.7596 (mtm) REVERT: D 51 MET cc_start: 0.8662 (ptt) cc_final: 0.8388 (ptt) REVERT: D 78 SER cc_start: 0.8271 (m) cc_final: 0.7933 (t) REVERT: E 72 GLU cc_start: 0.7834 (tp30) cc_final: 0.6934 (tm-30) REVERT: E 76 ASP cc_start: 0.7369 (m-30) cc_final: 0.6750 (m-30) REVERT: E 172 ASN cc_start: 0.7842 (t0) cc_final: 0.7449 (t0) REVERT: E 276 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7393 (mt) REVERT: F 101 SER cc_start: 0.9167 (t) cc_final: 0.8778 (p) outliers start: 25 outliers final: 15 residues processed: 194 average time/residue: 0.1044 time to fit residues: 28.9189 Evaluate side-chains 184 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 277 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 chunk 6 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.179055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.118461 restraints weight = 16457.078| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.38 r_work: 0.3237 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14026 Z= 0.162 Angle : 0.572 6.410 19573 Z= 0.331 Chirality : 0.043 0.245 2195 Planarity : 0.004 0.051 2042 Dihedral : 24.539 172.366 3008 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.07 % Allowed : 14.39 % Favored : 83.54 % 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 (0.23), residues: 1347 helix: 1.94 (0.20), residues: 640 sheet: -0.44 (0.36), residues: 214 loop : -0.92 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 116 TYR 0.015 0.001 TYR F 126 PHE 0.011 0.001 PHE A 89 TRP 0.026 0.001 TRP E 166 HIS 0.006 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (14026) covalent geometry : angle 0.57201 / 0.33 (19573) hydrogen bonds : bond 0.04057 / 2.74 ( 655) hydrogen bonds : angle 3.90288 / 2.78 ( 1812) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.301 Fit side-chains REVERT: A 3 MET cc_start: 0.8088 (ttt) cc_final: 0.7319 (ttt) REVERT: A 45 ARG cc_start: 0.7632 (mmm-85) cc_final: 0.7274 (mtp85) REVERT: B 130 PHE cc_start: 0.7186 (m-80) cc_final: 0.6751 (m-80) REVERT: B 272 MET cc_start: 0.7599 (mtp) cc_final: 0.7312 (mtp) REVERT: C 156 ARG cc_start: 0.7428 (mtm110) cc_final: 0.7081 (ptt90) REVERT: D 78 SER cc_start: 0.8263 (m) cc_final: 0.7907 (t) REVERT: E 72 GLU cc_start: 0.7611 (tp30) cc_final: 0.6683 (tm-30) REVERT: E 76 ASP cc_start: 0.7252 (m-30) cc_final: 0.6631 (m-30) REVERT: E 172 ASN cc_start: 0.7906 (t0) cc_final: 0.7548 (t0) REVERT: F 101 SER cc_start: 0.9105 (t) cc_final: 0.8710 (p) outliers start: 23 outliers final: 18 residues processed: 196 average time/residue: 0.1058 time to fit residues: 29.6421 Evaluate side-chains 188 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 277 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 30 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 143 optimal weight: 30.0000 chunk 68 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 104 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.178802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.116589 restraints weight = 18951.824| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.46 r_work: 0.3234 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14026 Z= 0.162 Angle : 0.575 7.537 19573 Z= 0.331 Chirality : 0.043 0.244 2195 Planarity : 0.004 0.050 2042 Dihedral : 24.570 172.339 3008 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.52 % Allowed : 14.75 % Favored : 82.73 % 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: 0.78 (0.23), residues: 1347 helix: 1.94 (0.20), residues: 640 sheet: -0.43 (0.36), residues: 214 loop : -0.94 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 116 TYR 0.016 0.001 TYR F 126 PHE 0.011 0.001 PHE A 89 TRP 0.010 0.001 TRP E 166 HIS 0.006 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (14026) covalent geometry : angle 0.57532 / 0.33 (19573) hydrogen bonds : bond 0.04019 / 2.73 ( 655) hydrogen bonds : angle 3.84484 / 2.74 ( 1812) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 0.298 Fit side-chains REVERT: A 45 ARG cc_start: 0.7659 (mmm-85) cc_final: 0.7314 (mtp85) REVERT: B 130 PHE cc_start: 0.7190 (m-80) cc_final: 0.6738 (m-80) REVERT: B 272 MET cc_start: 0.7592 (mtp) cc_final: 0.7292 (mtp) REVERT: C 156 ARG cc_start: 0.7393 (mtm110) cc_final: 0.7111 (ptt90) REVERT: D 78 SER cc_start: 0.8241 (m) cc_final: 0.7923 (t) REVERT: E 72 GLU cc_start: 0.7643 (tp30) cc_final: 0.6726 (tm-30) REVERT: E 76 ASP cc_start: 0.7284 (m-30) cc_final: 0.6653 (m-30) REVERT: E 172 ASN cc_start: 0.7911 (t0) cc_final: 0.7550 (t0) REVERT: E 246 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7285 (tm-30) REVERT: E 247 GLU cc_start: 0.7631 (mp0) cc_final: 0.7318 (pm20) REVERT: F 101 SER cc_start: 0.9104 (t) cc_final: 0.8709 (p) outliers start: 28 outliers final: 23 residues processed: 190 average time/residue: 0.1105 time to fit residues: 29.9392 Evaluate side-chains 188 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 277 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 111 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 142 optimal weight: 50.0000 chunk 113 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.179622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.116991 restraints weight = 16730.928| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.30 r_work: 0.3262 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14026 Z= 0.149 Angle : 0.563 6.347 19573 Z= 0.325 Chirality : 0.042 0.243 2195 Planarity : 0.004 0.049 2042 Dihedral : 24.615 172.306 3008 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.89 % Allowed : 15.65 % Favored : 82.46 % 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: 0.85 (0.23), residues: 1347 helix: 2.02 (0.20), residues: 640 sheet: -0.48 (0.36), residues: 216 loop : -0.89 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 116 TYR 0.014 0.001 TYR F 126 PHE 0.012 0.001 PHE A 89 TRP 0.010 0.001 TRP E 166 HIS 0.006 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (14026) covalent geometry : angle 0.56255 / 0.33 (19573) hydrogen bonds : bond 0.03859 / 2.62 ( 655) hydrogen bonds : angle 3.76146 / 2.68 ( 1812) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.265 Fit side-chains REVERT: A 45 ARG cc_start: 0.7611 (mmm-85) cc_final: 0.7276 (mtp85) REVERT: B 130 PHE cc_start: 0.7155 (m-80) cc_final: 0.6704 (m-80) REVERT: C 156 ARG cc_start: 0.7379 (mtm110) cc_final: 0.7123 (ptt90) REVERT: D 78 SER cc_start: 0.8277 (m) cc_final: 0.7923 (t) REVERT: E 140 MET cc_start: 0.6961 (mmm) cc_final: 0.6714 (mmt) REVERT: E 172 ASN cc_start: 0.7844 (t0) cc_final: 0.7441 (t0) REVERT: E 246 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7525 (tm-30) REVERT: E 247 GLU cc_start: 0.7663 (mp0) cc_final: 0.7393 (pm20) REVERT: F 101 SER cc_start: 0.9089 (t) cc_final: 0.8681 (p) REVERT: F 116 ARG cc_start: 0.7775 (mmm-85) cc_final: 0.7558 (mtp-110) outliers start: 21 outliers final: 18 residues processed: 195 average time/residue: 0.1026 time to fit residues: 28.7558 Evaluate side-chains 188 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 277 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 105 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 112 optimal weight: 0.3980 chunk 110 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN ** D 24 GLN ** 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 = 0.4211 r_free = 0.4211 target = 0.179965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.119201 restraints weight = 18446.151| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.39 r_work: 0.3270 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14026 Z= 0.150 Angle : 0.569 6.645 19573 Z= 0.327 Chirality : 0.042 0.244 2195 Planarity : 0.004 0.049 2042 Dihedral : 24.642 172.182 3008 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.80 % Allowed : 15.74 % Favored : 82.46 % 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: 0.86 (0.23), residues: 1347 helix: 2.02 (0.20), residues: 640 sheet: -0.46 (0.36), residues: 216 loop : -0.87 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 152 TYR 0.016 0.001 TYR F 126 PHE 0.012 0.001 PHE A 89 TRP 0.007 0.001 TRP E 166 HIS 0.006 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (14026) covalent geometry : angle 0.56874 / 0.33 (19573) hydrogen bonds : bond 0.03852 / 2.61 ( 655) hydrogen bonds : angle 3.75654 / 2.68 ( 1812) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 0.364 Fit side-chains REVERT: A 45 ARG cc_start: 0.7595 (mmm-85) cc_final: 0.7245 (mtp85) REVERT: B 130 PHE cc_start: 0.7157 (m-80) cc_final: 0.6726 (m-80) REVERT: C 156 ARG cc_start: 0.7417 (mtm110) cc_final: 0.7169 (ptt90) REVERT: D 78 SER cc_start: 0.8347 (m) cc_final: 0.7933 (t) REVERT: E 172 ASN cc_start: 0.7878 (t0) cc_final: 0.7461 (t0) REVERT: F 101 SER cc_start: 0.9101 (t) cc_final: 0.8676 (p) REVERT: F 116 ARG cc_start: 0.7785 (mmm-85) cc_final: 0.7576 (mtp-110) outliers start: 20 outliers final: 20 residues processed: 191 average time/residue: 0.1058 time to fit residues: 29.3088 Evaluate side-chains 193 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 277 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 88 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 72 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 145 optimal weight: 50.0000 chunk 123 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.178104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.116723 restraints weight = 18563.649| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.44 r_work: 0.3233 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14026 Z= 0.165 Angle : 0.580 7.015 19573 Z= 0.332 Chirality : 0.043 0.245 2195 Planarity : 0.004 0.051 2042 Dihedral : 24.642 172.267 3008 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.89 % Allowed : 16.10 % Favored : 82.01 % 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: 0.80 (0.23), residues: 1347 helix: 1.98 (0.20), residues: 640 sheet: -0.49 (0.36), residues: 216 loop : -0.92 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 144 TYR 0.016 0.001 TYR F 126 PHE 0.011 0.001 PHE A 89 TRP 0.008 0.001 TRP B 296 HIS 0.007 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (14026) covalent geometry : angle 0.57953 / 0.33 (19573) hydrogen bonds : bond 0.04000 / 2.73 ( 655) hydrogen bonds : angle 3.80163 / 2.71 ( 1812) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 0.379 Fit side-chains REVERT: A 45 ARG cc_start: 0.7641 (mmm-85) cc_final: 0.7322 (mtp85) REVERT: B 130 PHE cc_start: 0.7118 (m-80) cc_final: 0.6685 (m-80) REVERT: C 156 ARG cc_start: 0.7484 (mtm110) cc_final: 0.7210 (ptt90) REVERT: D 78 SER cc_start: 0.8289 (m) cc_final: 0.7902 (t) REVERT: E 172 ASN cc_start: 0.7931 (t0) cc_final: 0.7491 (t0) REVERT: E 247 GLU cc_start: 0.7856 (mp0) cc_final: 0.7572 (pm20) REVERT: F 36 ASP cc_start: 0.7821 (m-30) cc_final: 0.7489 (m-30) REVERT: F 101 SER cc_start: 0.9103 (t) cc_final: 0.8643 (p) REVERT: F 116 ARG cc_start: 0.7809 (mmm-85) cc_final: 0.7584 (mtp-110) outliers start: 21 outliers final: 21 residues processed: 188 average time/residue: 0.1083 time to fit residues: 29.2796 Evaluate side-chains 194 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 277 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 76 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 54 optimal weight: 0.2980 chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 108 optimal weight: 0.0370 chunk 2 optimal weight: 0.3980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.180610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.119071 restraints weight = 16923.050| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.29 r_work: 0.3309 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14026 Z= 0.130 Angle : 0.562 7.421 19573 Z= 0.322 Chirality : 0.042 0.244 2195 Planarity : 0.004 0.048 2042 Dihedral : 24.601 171.378 3008 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.62 % Allowed : 16.55 % Favored : 81.83 % 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 (0.23), residues: 1347 helix: 2.04 (0.20), residues: 641 sheet: -0.42 (0.36), residues: 216 loop : -0.84 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 144 TYR 0.015 0.001 TYR F 126 PHE 0.015 0.001 PHE A 89 TRP 0.008 0.001 TRP E 166 HIS 0.005 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 (14026) covalent geometry : angle 0.56156 / 0.32 (19573) hydrogen bonds : bond 0.03687 / 2.52 ( 655) hydrogen bonds : angle 3.71013 / 2.64 ( 1812) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4269.47 seconds wall clock time: 73 minutes 15.78 seconds (4395.78 seconds total)