Starting phenix.real_space_refine on Thu Aug 6 05:35:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fyb_29563/08_2026/8fyb_29563.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fyb_29563/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fyb_29563/08_2026/8fyb_29563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fyb_29563/08_2026/8fyb_29563.map" model { file = "/net/cci-nas-00/data/ceres_data/8fyb_29563/08_2026/8fyb_29563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fyb_29563/08_2026/8fyb_29563.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.031 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-2.2rc3-6140/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: 3.59, per 1000 atoms: 0.27 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: 1.27 Conformation dependent library (CDL) restraints added in 605.4 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: 1.57 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: 2.23 Time building geometry restraints manager: 1.68 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: 18944 1.82 - 3.64: 583 3.64 - 5.47: 38 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.180 Find NCS groups from input model: 0.240 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.020 ------------------------------------------------------------------------------- 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= 0.387 Angle : 0.674 9.109 19573 Z= 0.510 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 0.67445 / 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 : 0.306 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: 0.7964 (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: 0.7647 (t0) REVERT: E 175 ASP cc_start: 0.7559 (t70) cc_final: 0.7092 (m-30) REVERT: E 193 LEU cc_start: 0.8391 (tp) cc_final: 0.8149 (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: 0.8701 (p) REVERT: F 275 ASP cc_start: 0.8134 (m-30) cc_final: 0.7842 (m-30) outliers start: 1 outliers final: 0 residues processed: 295 average time/residue: 0.1191 time to fit residues: 48.5996 Evaluate side-chains 187 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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: 0.6980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 7.9990 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: 0.7980 chunk 55 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4230 r_free = 0.4230 target = 0.181917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.117086 restraints weight = 15514.596| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.19 r_work: 0.3321 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14026 Z= 0.167 Angle : 0.651 6.809 19573 Z= 0.370 Chirality : 0.046 0.287 2195 Planarity : 0.004 0.043 2042 Dihedral : 24.120 178.643 3008 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.17 % Allowed : 8.99 % Favored : 89.84 % 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: 1.72 (0.20), residues: 641 sheet: -0.36 (0.36), residues: 214 loop : -0.86 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 45 TYR 0.012 0.002 TYR E 223 PHE 0.009 0.001 PHE B 212 TRP 0.014 0.001 TRP C 296 HIS 0.007 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.17 (14026) covalent geometry : angle 0.65084 / 0.37 (19573) hydrogen bonds : bond 0.05170 / 3.45 ( 655) hydrogen bonds : angle 4.37513 / 3.11 ( 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 225 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 212 time to evaluate : 0.444 Fit side-chains REVERT: A 9 LYS cc_start: 0.8868 (ttpt) cc_final: 0.8664 (ttpp) REVERT: A 45 ARG cc_start: 0.7640 (mmm-85) cc_final: 0.7364 (mtp85) REVERT: A 73 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7835 (tp30) REVERT: B 128 MET cc_start: 0.7654 (ptm) cc_final: 0.7448 (ptp) REVERT: B 138 LEU cc_start: 0.8652 (mp) cc_final: 0.8435 (tp) REVERT: B 175 ASP cc_start: 0.8079 (t0) cc_final: 0.7857 (t0) REVERT: B 281 GLU cc_start: 0.8047 (mp0) cc_final: 0.7744 (mp0) REVERT: B 289 GLU cc_start: 0.8209 (tp30) cc_final: 0.7789 (tp30) REVERT: C 156 ARG cc_start: 0.7579 (mtm110) cc_final: 0.7255 (ptt90) REVERT: C 162 TYR cc_start: 0.8203 (m-80) cc_final: 0.7818 (m-80) REVERT: D 78 SER cc_start: 0.8244 (m) cc_final: 0.7960 (t) REVERT: E 72 GLU cc_start: 0.7768 (tp30) cc_final: 0.6798 (tp30) REVERT: E 76 ASP cc_start: 0.7285 (m-30) cc_final: 0.6765 (m-30) REVERT: E 124 ARG cc_start: 0.7611 (ttp-110) cc_final: 0.6845 (ttp-170) REVERT: E 155 TYR cc_start: 0.7367 (m-80) cc_final: 0.7155 (m-80) REVERT: E 172 ASN cc_start: 0.7830 (t0) cc_final: 0.7458 (t0) REVERT: E 193 LEU cc_start: 0.8595 (tp) cc_final: 0.8388 (tp) REVERT: F 101 SER cc_start: 0.9195 (t) cc_final: 0.8869 (p) REVERT: F 275 ASP cc_start: 0.8279 (m-30) cc_final: 0.7883 (m-30) outliers start: 13 outliers final: 8 residues processed: 220 average time/residue: 0.1334 time to fit residues: 41.8314 Evaluate side-chains 196 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 188 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain C residue 72 GLU 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 41 optimal weight: 0.0670 chunk 39 optimal weight: 0.4980 chunk 3 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 183 ASN ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 ASN E 183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.180521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.114640 restraints weight = 15929.010| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.29 r_work: 0.3285 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14026 Z= 0.169 Angle : 0.603 6.543 19573 Z= 0.345 Chirality : 0.044 0.260 2195 Planarity : 0.004 0.050 2042 Dihedral : 24.413 174.327 3008 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.35 % Allowed : 11.87 % 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: 0.72 (0.23), residues: 1347 helix: 1.77 (0.20), residues: 642 sheet: -0.42 (0.36), residues: 216 loop : -0.82 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 49 TYR 0.020 0.001 TYR E 223 PHE 0.009 0.001 PHE E 239 TRP 0.007 0.001 TRP E 296 HIS 0.009 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 (14026) covalent geometry : angle 0.60252 / 0.34 (19573) hydrogen bonds : bond 0.04515 / 3.01 ( 655) hydrogen bonds : angle 4.15172 / 2.97 ( 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 211 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 0.448 Fit side-chains REVERT: A 45 ARG cc_start: 0.7767 (mmm-85) cc_final: 0.7443 (mtp85) REVERT: B 138 LEU cc_start: 0.8641 (mp) cc_final: 0.8366 (tp) REVERT: B 175 ASP cc_start: 0.8134 (t0) cc_final: 0.7917 (t0) REVERT: B 281 GLU cc_start: 0.8044 (mp0) cc_final: 0.7782 (mp0) REVERT: B 289 GLU cc_start: 0.8206 (tp30) cc_final: 0.7701 (tp30) REVERT: C 125 MET cc_start: 0.7425 (mtt) cc_final: 0.7216 (mtp) REVERT: C 152 ARG cc_start: 0.7803 (mtm-85) cc_final: 0.7519 (mtm-85) REVERT: C 156 ARG cc_start: 0.7584 (mtm110) cc_final: 0.7261 (ptt90) REVERT: C 162 TYR cc_start: 0.8243 (m-80) cc_final: 0.7858 (m-80) REVERT: C 253 GLN cc_start: 0.7864 (mt0) cc_final: 0.7496 (mm-40) REVERT: C 300 GLU cc_start: 0.8064 (tp30) cc_final: 0.7810 (tp30) REVERT: D 51 MET cc_start: 0.8464 (ptt) cc_final: 0.8237 (ptt) REVERT: D 78 SER cc_start: 0.8316 (m) cc_final: 0.8001 (t) REVERT: E 72 GLU cc_start: 0.7842 (tp30) cc_final: 0.7007 (tm-30) REVERT: E 76 ASP cc_start: 0.7247 (m-30) cc_final: 0.6615 (m-30) REVERT: E 155 TYR cc_start: 0.7485 (m-10) cc_final: 0.7238 (m-80) REVERT: E 172 ASN cc_start: 0.7926 (t0) cc_final: 0.7580 (t0) REVERT: F 101 SER cc_start: 0.9208 (t) cc_final: 0.8848 (p) outliers start: 15 outliers final: 9 residues processed: 205 average time/residue: 0.1272 time to fit residues: 37.3437 Evaluate side-chains 186 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 177 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 146 HIS Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain F residue 12 SER 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: 9.9990 chunk 113 optimal weight: 0.2980 chunk 2 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 127 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.181574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.120010 restraints weight = 16697.711| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.35 r_work: 0.3291 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14026 Z= 0.143 Angle : 0.580 6.526 19573 Z= 0.333 Chirality : 0.044 0.270 2195 Planarity : 0.004 0.049 2042 Dihedral : 24.418 173.376 3008 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.44 % Allowed : 13.04 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.23), residues: 1347 helix: 1.86 (0.20), residues: 642 sheet: -0.43 (0.36), residues: 216 loop : -0.86 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 116 TYR 0.018 0.001 TYR F 126 PHE 0.010 0.001 PHE A 89 TRP 0.013 0.001 TRP C 296 HIS 0.006 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (14026) covalent geometry : angle 0.58024 / 0.33 (19573) hydrogen bonds : bond 0.04084 / 2.72 ( 655) hydrogen bonds : angle 4.00713 / 2.86 ( 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 205 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 0.446 Fit side-chains REVERT: A 45 ARG cc_start: 0.7536 (mmm-85) cc_final: 0.7171 (mtp85) REVERT: B 138 LEU cc_start: 0.8615 (mp) cc_final: 0.8383 (tp) REVERT: B 175 ASP cc_start: 0.8021 (t0) cc_final: 0.7813 (t0) REVERT: B 272 MET cc_start: 0.7519 (mtp) cc_final: 0.7202 (mtp) REVERT: B 289 GLU cc_start: 0.8142 (tp30) cc_final: 0.7623 (tp30) REVERT: C 125 MET cc_start: 0.7296 (mtt) cc_final: 0.6976 (mtp) REVERT: C 152 ARG cc_start: 0.7796 (mtm-85) cc_final: 0.7581 (mtm-85) REVERT: C 253 GLN cc_start: 0.7697 (mt0) cc_final: 0.7294 (mm-40) REVERT: C 261 ASP cc_start: 0.8160 (t0) cc_final: 0.7850 (t0) REVERT: D 78 SER cc_start: 0.8187 (m) cc_final: 0.7835 (t) REVERT: E 72 GLU cc_start: 0.7573 (tp30) cc_final: 0.6659 (tm-30) REVERT: E 76 ASP cc_start: 0.7175 (m-30) cc_final: 0.6570 (m-30) REVERT: E 155 TYR cc_start: 0.7365 (m-10) cc_final: 0.7105 (m-80) REVERT: E 172 ASN cc_start: 0.7999 (t0) cc_final: 0.7624 (t0) REVERT: F 101 SER cc_start: 0.9165 (t) cc_final: 0.8797 (p) REVERT: F 104 PHE cc_start: 0.8577 (m-10) cc_final: 0.8312 (m-10) outliers start: 16 outliers final: 11 residues processed: 199 average time/residue: 0.1151 time to fit residues: 33.4912 Evaluate side-chains 186 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 244 GLU Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 160 LYS 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: 1.9990 chunk 134 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.4182 r_free = 0.4182 target = 0.177151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.115924 restraints weight = 16294.893| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.30 r_work: 0.3226 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 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 = 0.3231 r_free = 0.3231 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: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14026 Z= 0.216 Angle : 0.619 6.409 19573 Z= 0.351 Chirality : 0.044 0.270 2195 Planarity : 0.004 0.051 2042 Dihedral : 24.545 173.546 3008 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.43 % Allowed : 13.58 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.23), residues: 1347 helix: 1.81 (0.20), residues: 639 sheet: -0.51 (0.37), residues: 212 loop : -0.90 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 116 TYR 0.017 0.002 TYR F 126 PHE 0.012 0.002 PHE E 239 TRP 0.013 0.002 TRP E 166 HIS 0.008 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 (14026) covalent geometry : angle 0.61931 / 0.35 (19573) hydrogen bonds : bond 0.04515 / 3.06 ( 655) hydrogen bonds : angle 4.07387 / 2.91 ( 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 194 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.395 Fit side-chains REVERT: A 3 MET cc_start: 0.8194 (ttt) cc_final: 0.7457 (ttt) REVERT: A 45 ARG cc_start: 0.7586 (mmm-85) cc_final: 0.7229 (mtp85) REVERT: B 130 PHE cc_start: 0.7174 (m-80) cc_final: 0.6751 (m-80) REVERT: B 138 LEU cc_start: 0.8693 (mp) cc_final: 0.8430 (tp) REVERT: C 156 ARG cc_start: 0.7578 (mtm110) cc_final: 0.7277 (ptt90) REVERT: D 78 SER cc_start: 0.8198 (m) cc_final: 0.7868 (t) REVERT: E 72 GLU cc_start: 0.7593 (tp30) cc_final: 0.6723 (tm-30) REVERT: E 76 ASP cc_start: 0.7173 (m-30) cc_final: 0.6498 (m-30) REVERT: E 140 MET cc_start: 0.6484 (mmt) cc_final: 0.6202 (mmt) REVERT: E 172 ASN cc_start: 0.7947 (t0) cc_final: 0.7580 (t0) REVERT: F 101 SER cc_start: 0.9127 (t) cc_final: 0.8748 (p) outliers start: 27 outliers final: 20 residues processed: 182 average time/residue: 0.1163 time to fit residues: 30.4077 Evaluate side-chains 181 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 234 THR 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 98 LEU Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 163 ASN 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 48 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: 0.9990 chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4210 r_free = 0.4210 target = 0.179898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.119296 restraints weight = 15872.077| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.25 r_work: 0.3266 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 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 = 0.3271 r_free = 0.3271 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: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2568 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= 0.151 Angle : 0.571 6.415 19573 Z= 0.329 Chirality : 0.043 0.270 2195 Planarity : 0.004 0.050 2042 Dihedral : 24.524 173.049 3008 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.53 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: 1.93 (0.20), residues: 640 sheet: -0.47 (0.36), residues: 216 loop : -0.88 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 116 TYR 0.015 0.001 TYR E 223 PHE 0.011 0.001 PHE A 89 TRP 0.008 0.001 TRP E 296 HIS 0.006 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (14026) covalent geometry : angle 0.57126 / 0.33 (19573) hydrogen bonds : bond 0.04003 / 2.70 ( 655) hydrogen bonds : angle 3.92734 / 2.80 ( 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 206 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.449 Fit side-chains REVERT: A 3 MET cc_start: 0.8033 (ttt) cc_final: 0.7276 (ttt) REVERT: A 45 ARG cc_start: 0.7582 (mmm-85) cc_final: 0.7231 (mtp85) REVERT: C 156 ARG cc_start: 0.7537 (mtm110) cc_final: 0.7165 (ptt90) REVERT: C 261 ASP cc_start: 0.8190 (t0) cc_final: 0.7945 (t0) REVERT: D 78 SER cc_start: 0.8216 (m) cc_final: 0.7896 (t) REVERT: E 72 GLU cc_start: 0.7590 (tp30) cc_final: 0.6677 (tm-30) REVERT: E 76 ASP cc_start: 0.7238 (m-30) cc_final: 0.6632 (m-30) REVERT: E 172 ASN cc_start: 0.7927 (t0) cc_final: 0.7553 (t0) REVERT: F 101 SER cc_start: 0.9121 (t) cc_final: 0.8746 (p) REVERT: F 116 ARG cc_start: 0.7778 (mmm-85) cc_final: 0.7565 (mtp-110) outliers start: 23 outliers final: 17 residues processed: 197 average time/residue: 0.1040 time to fit residues: 29.6966 Evaluate side-chains 182 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 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 E residue 160 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 30 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 143 optimal weight: 30.0000 chunk 68 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 277 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.177550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.115028 restraints weight = 16777.600| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.44 r_work: 0.3220 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14026 Z= 0.200 Angle : 0.607 6.386 19573 Z= 0.345 Chirality : 0.045 0.266 2195 Planarity : 0.004 0.049 2042 Dihedral : 24.611 173.592 3008 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.61 % Allowed : 14.84 % Favored : 82.55 % 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: 0.73 (0.23), residues: 1347 helix: 1.90 (0.21), residues: 639 sheet: -0.49 (0.36), residues: 216 loop : -0.94 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 116 TYR 0.017 0.002 TYR F 126 PHE 0.011 0.001 PHE E 239 TRP 0.008 0.001 TRP B 83 HIS 0.006 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 (14026) covalent geometry : angle 0.60723 / 0.35 (19573) hydrogen bonds : bond 0.04332 / 2.93 ( 655) hydrogen bonds : angle 4.00253 / 2.86 ( 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 198 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.357 Fit side-chains REVERT: A 45 ARG cc_start: 0.7613 (mmm-85) cc_final: 0.7276 (mtp85) REVERT: B 130 PHE cc_start: 0.7191 (m-80) cc_final: 0.6752 (m-80) REVERT: B 272 MET cc_start: 0.7578 (mtp) cc_final: 0.7294 (mtp) REVERT: C 156 ARG cc_start: 0.7536 (mtm110) cc_final: 0.7125 (ptt90) REVERT: D 78 SER cc_start: 0.8216 (m) cc_final: 0.7868 (t) REVERT: E 72 GLU cc_start: 0.7583 (tp30) cc_final: 0.6674 (tm-30) REVERT: E 76 ASP cc_start: 0.7271 (m-30) cc_final: 0.6635 (m-30) REVERT: E 172 ASN cc_start: 0.7917 (t0) cc_final: 0.7520 (t0) REVERT: E 246 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7452 (tm-30) REVERT: E 247 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7239 (pm20) REVERT: F 101 SER cc_start: 0.9128 (t) cc_final: 0.8714 (p) outliers start: 29 outliers final: 22 residues processed: 185 average time/residue: 0.1052 time to fit residues: 27.8425 Evaluate side-chains 186 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 35 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 234 THR 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 160 LYS Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 247 GLU 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 237 ILE 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: 0.5980 chunk 86 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 142 optimal weight: 50.0000 chunk 113 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 118 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 277 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.179512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.117618 restraints weight = 16543.103| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.37 r_work: 0.3268 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 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 = 0.3269 r_free = 0.3269 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: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2804 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= 0.142 Angle : 0.571 6.365 19573 Z= 0.329 Chirality : 0.043 0.267 2195 Planarity : 0.004 0.048 2042 Dihedral : 24.617 173.060 3008 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.25 % Allowed : 14.93 % Favored : 82.82 % 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: 0.81 (0.23), residues: 1347 helix: 1.97 (0.20), residues: 641 sheet: -0.52 (0.36), residues: 216 loop : -0.89 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 116 TYR 0.015 0.001 TYR F 126 PHE 0.012 0.001 PHE A 89 TRP 0.008 0.001 TRP B 83 HIS 0.005 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (14026) covalent geometry : angle 0.57095 / 0.33 (19573) hydrogen bonds : bond 0.03902 / 2.65 ( 655) hydrogen bonds : angle 3.87507 / 2.77 ( 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 199 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.294 Fit side-chains REVERT: A 45 ARG cc_start: 0.7561 (mmm-85) cc_final: 0.7240 (mtp85) REVERT: B 130 PHE cc_start: 0.7179 (m-80) cc_final: 0.6728 (m-80) REVERT: C 156 ARG cc_start: 0.7504 (mtm110) cc_final: 0.7237 (ptt90) REVERT: D 78 SER cc_start: 0.8253 (m) cc_final: 0.7920 (t) REVERT: E 172 ASN cc_start: 0.7931 (t0) cc_final: 0.7571 (t0) REVERT: F 101 SER cc_start: 0.9123 (t) cc_final: 0.8707 (p) outliers start: 25 outliers final: 22 residues processed: 190 average time/residue: 0.1068 time to fit residues: 29.0374 Evaluate side-chains 187 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 277 GLN Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 147 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 160 LYS 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 237 ILE 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: 0.9980 chunk 13 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4202 r_free = 0.4202 target = 0.179275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.117832 restraints weight = 19544.203| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.42 r_work: 0.3251 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14026 Z= 0.149 Angle : 0.584 7.998 19573 Z= 0.333 Chirality : 0.043 0.315 2195 Planarity : 0.004 0.059 2042 Dihedral : 24.638 173.066 3008 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.98 % Allowed : 15.83 % Favored : 82.19 % 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: 0.83 (0.23), residues: 1347 helix: 1.99 (0.20), residues: 641 sheet: -0.46 (0.36), residues: 216 loop : -0.90 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 144 TYR 0.016 0.001 TYR F 126 PHE 0.012 0.001 PHE A 89 TRP 0.007 0.001 TRP B 83 HIS 0.005 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (14026) covalent geometry : angle 0.58376 / 0.33 (19573) hydrogen bonds : bond 0.03902 / 2.65 ( 655) hydrogen bonds : angle 3.84931 / 2.75 ( 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 194 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.288 Fit side-chains REVERT: A 45 ARG cc_start: 0.7638 (mmm-85) cc_final: 0.7321 (mtp85) REVERT: B 130 PHE cc_start: 0.7162 (m-80) cc_final: 0.6707 (m-80) REVERT: D 78 SER cc_start: 0.8253 (m) cc_final: 0.7933 (t) REVERT: E 172 ASN cc_start: 0.7963 (t0) cc_final: 0.7576 (t0) REVERT: E 246 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7612 (tm-30) REVERT: E 247 GLU cc_start: 0.7786 (mp0) cc_final: 0.7517 (pm20) REVERT: F 101 SER cc_start: 0.9132 (t) cc_final: 0.8711 (p) outliers start: 22 outliers final: 21 residues processed: 184 average time/residue: 0.1053 time to fit residues: 27.4318 Evaluate side-chains 189 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 35 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 147 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 160 LYS 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 237 ILE 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: 3.9990 chunk 70 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 145 optimal weight: 50.0000 chunk 123 optimal weight: 0.0170 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 277 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 = 0.4217 r_free = 0.4217 target = 0.180574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.117652 restraints weight = 19027.396| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.46 r_work: 0.3268 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 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 = 0.3276 r_free = 0.3276 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: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14026 Z= 0.136 Angle : 0.566 6.900 19573 Z= 0.325 Chirality : 0.043 0.268 2195 Planarity : 0.004 0.069 2042 Dihedral : 24.603 172.630 3008 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.07 % Allowed : 15.74 % Favored : 82.19 % 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: 0.87 (0.23), residues: 1347 helix: 2.01 (0.20), residues: 641 sheet: -0.44 (0.36), residues: 215 loop : -0.85 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 144 TYR 0.015 0.001 TYR E 223 PHE 0.012 0.001 PHE A 89 TRP 0.011 0.001 TRP D 44 HIS 0.006 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (14026) covalent geometry : angle 0.56633 / 0.32 (19573) hydrogen bonds : bond 0.03796 / 2.59 ( 655) hydrogen bonds : angle 3.82640 / 2.73 ( 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 203 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 0.296 Fit side-chains REVERT: A 45 ARG cc_start: 0.7599 (mmm-85) cc_final: 0.7287 (mtp85) REVERT: B 130 PHE cc_start: 0.7023 (m-80) cc_final: 0.6574 (m-80) REVERT: B 272 MET cc_start: 0.7783 (mtp) cc_final: 0.7447 (mtp) REVERT: B 281 GLU cc_start: 0.7959 (mp0) cc_final: 0.7487 (mp0) REVERT: C 156 ARG cc_start: 0.7574 (mtm110) cc_final: 0.7343 (ptt90) REVERT: D 73 GLU cc_start: 0.7915 (tp30) cc_final: 0.7649 (tp30) REVERT: D 78 SER cc_start: 0.8242 (m) cc_final: 0.7924 (t) REVERT: E 140 MET cc_start: 0.6916 (mmm) cc_final: 0.6684 (mmt) REVERT: E 172 ASN cc_start: 0.8046 (t0) cc_final: 0.7643 (t0) REVERT: F 100 ARG cc_start: 0.8195 (mtm180) cc_final: 0.7907 (mtm180) REVERT: F 101 SER cc_start: 0.9113 (t) cc_final: 0.8674 (p) outliers start: 23 outliers final: 21 residues processed: 192 average time/residue: 0.1034 time to fit residues: 28.3972 Evaluate side-chains 196 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 35 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 147 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 160 LYS 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 237 ILE 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: 1.9990 chunk 64 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 75 optimal weight: 0.0980 chunk 139 optimal weight: 9.9990 chunk 51 optimal weight: 0.0570 chunk 108 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 277 GLN ** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.180982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.117881 restraints weight = 15972.324| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.28 r_work: 0.3302 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 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 = 0.3162 r_free = 0.3162 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: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14026 Z= 0.134 Angle : 0.571 7.147 19573 Z= 0.325 Chirality : 0.043 0.297 2195 Planarity : 0.004 0.064 2042 Dihedral : 24.593 172.354 3008 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.07 % Allowed : 15.56 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.23), residues: 1347 helix: 2.04 (0.20), residues: 641 sheet: -0.40 (0.36), residues: 215 loop : -0.85 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 144 TYR 0.016 0.001 TYR F 126 PHE 0.013 0.001 PHE A 89 TRP 0.008 0.001 TRP C 296 HIS 0.006 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (14026) covalent geometry : angle 0.57095 / 0.33 (19573) hydrogen bonds : bond 0.03756 / 2.56 ( 655) hydrogen bonds : angle 3.79661 / 2.71 ( 1812) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4467.94 seconds wall clock time: 76 minutes 39.85 seconds (4599.85 seconds total)