Starting phenix.real_space_refine on Thu Aug 6 22:18:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x32_38026/08_2026/8x32_38026.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x32_38026/08_2026/8x32_38026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x32_38026/08_2026/8x32_38026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x32_38026/08_2026/8x32_38026.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x32_38026/08_2026/8x32_38026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x32_38026/08_2026/8x32_38026.map" } resolution = 4.4 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= 0.022 sd= 0.415 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 1064 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 290 5.49 5 S 23 5.16 5 C 9819 2.51 5 N 3043 2.21 5 O 3769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 16944 Number of models: 1 Model: "" Number of chains: 14 Chain: "L" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 205 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "N" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 604 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain breaks: 1 Chain: "K" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2309 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 261} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1919 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 8, 'TRANS': 221} Chain breaks: 2 Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2990 Classifications: {'DNA': 146} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2990 Classifications: {'DNA': 146} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 145} Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 750 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 746 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Time building chain proxies: 2.54, per 1000 atoms: 0.15 Number of scatterers: 16944 At special positions: 0 Unit cell: (134.16, 136.24, 127.92, 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 23 16.00 P 290 15.00 O 3769 8.00 N 3043 7.00 C 9819 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: 1.20 Conformation dependent library (CDL) restraints added in 495.3 milliseconds 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2578 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 5 sheets defined 52.4% alpha, 2.7% beta 143 base pairs and 226 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'N' and resid 3 through 10 removed outlier: 4.260A pdb=" N LEU N 7 " --> pdb=" O PRO N 3 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU N 8 " --> pdb=" O SER N 4 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN N 9 " --> pdb=" O LEU N 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 29 removed outlier: 4.259A pdb=" N LEU N 25 " --> pdb=" O PHE N 21 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLU N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N GLU N 27 " --> pdb=" O TYR N 23 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE N 28 " --> pdb=" O LEU N 24 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY N 29 " --> pdb=" O LEU N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 39 removed outlier: 3.772A pdb=" N GLU N 38 " --> pdb=" O LYS N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 87 removed outlier: 4.072A pdb=" N LYS N 86 " --> pdb=" O LEU N 82 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N CYS N 87 " --> pdb=" O GLN N 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 82 through 87' Processing helix chain 'N' and resid 87 through 92 Processing helix chain 'N' and resid 94 through 96 No H-bonds generated for 'chain 'N' and resid 94 through 96' Processing helix chain 'N' and resid 97 through 105 removed outlier: 4.077A pdb=" N LEU N 101 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN N 102 " --> pdb=" O ALA N 98 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LYS N 103 " --> pdb=" O ARG N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 111 removed outlier: 4.029A pdb=" N ALA N 109 " --> pdb=" O GLU N 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 212 through 217 Processing helix chain 'K' and resid 246 through 259 removed outlier: 4.018A pdb=" N ASN K 250 " --> pdb=" O THR K 246 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU K 251 " --> pdb=" O TRP K 247 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N CYS K 252 " --> pdb=" O CYS K 248 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU K 253 " --> pdb=" O ARG K 249 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU K 254 " --> pdb=" O ASN K 250 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER K 255 " --> pdb=" O LEU K 251 " (cutoff:3.500A) Processing helix chain 'K' and resid 314 through 318 Processing helix chain 'K' and resid 323 through 332 removed outlier: 3.744A pdb=" N LEU K 327 " --> pdb=" O PHE K 323 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS K 329 " --> pdb=" O TYR K 325 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LYS K 330 " --> pdb=" O GLU K 326 " (cutoff:3.500A) Processing helix chain 'K' and resid 345 through 363 removed outlier: 4.863A pdb=" N ALA K 351 " --> pdb=" O LEU K 347 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP K 355 " --> pdb=" O ALA K 351 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR K 356 " --> pdb=" O TYR K 352 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU K 357 " --> pdb=" O TRP K 353 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE K 358 " --> pdb=" O SER K 354 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU K 360 " --> pdb=" O THR K 356 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU K 361 " --> pdb=" O LEU K 357 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU K 363 " --> pdb=" O THR K 359 " (cutoff:3.500A) Processing helix chain 'K' and resid 380 through 385 Processing helix chain 'K' and resid 388 through 392 Processing helix chain 'K' and resid 414 through 419 Processing helix chain 'M' and resid 153 through 159 Processing helix chain 'M' and resid 165 through 170 removed outlier: 4.009A pdb=" N GLU M 169 " --> pdb=" O ASP M 165 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 196 removed outlier: 3.884A pdb=" N LEU M 192 " --> pdb=" O GLU M 188 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER M 194 " --> pdb=" O GLU M 190 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE M 196 " --> pdb=" O LEU M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 214 removed outlier: 3.864A pdb=" N ILE M 214 " --> pdb=" O PRO M 211 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 219 Processing helix chain 'M' and resid 220 through 225 removed outlier: 3.886A pdb=" N ILE M 225 " --> pdb=" O LYS M 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 255 through 259 removed outlier: 3.873A pdb=" N GLN M 258 " --> pdb=" O PRO M 255 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 272 removed outlier: 3.775A pdb=" N ILE M 268 " --> pdb=" O LEU M 264 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS M 270 " --> pdb=" O GLN M 266 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 275 No H-bonds generated for 'chain 'M' and resid 273 through 275' Processing helix chain 'M' and resid 276 through 281 removed outlier: 4.090A pdb=" N GLU M 281 " --> pdb=" O ASP M 277 " (cutoff:3.500A) Processing helix chain 'M' and resid 283 through 287 Processing helix chain 'M' and resid 328 through 332 removed outlier: 3.659A pdb=" N SER M 331 " --> pdb=" O ILE M 328 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN M 332 " --> pdb=" O LEU M 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 328 through 332' Processing helix chain 'M' and resid 333 through 339 removed outlier: 3.740A pdb=" N ALA M 336 " --> pdb=" O ARG M 333 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS M 338 " --> pdb=" O ARG M 335 " (cutoff:3.500A) Processing helix chain 'M' and resid 344 through 349 Processing helix chain 'M' and resid 352 through 357 Processing helix chain 'A' and resid 44 through 57 removed outlier: 4.129A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 4.236A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.781A pdb=" N ILE A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 removed outlier: 3.975A pdb=" N ILE A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 32 through 40 Processing helix chain 'B' and resid 50 through 76 Processing helix chain 'B' and resid 83 through 90 Processing helix chain 'C' and resid 28 through 37 Processing helix chain 'C' and resid 48 through 61 removed outlier: 3.751A pdb=" N ALA C 55 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL C 56 " --> pdb=" O TYR C 52 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 69 through 73 removed outlier: 3.668A pdb=" N ALA C 72 " --> pdb=" O GLY C 69 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS C 73 " --> pdb=" O ASN C 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 69 through 73' Processing helix chain 'C' and resid 80 through 85 Processing helix chain 'C' and resid 91 through 99 removed outlier: 3.937A pdb=" N GLU C 94 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ASP C 96 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 51 Processing helix chain 'D' and resid 58 through 87 Processing helix chain 'D' and resid 94 through 104 Processing helix chain 'D' and resid 107 through 127 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.501A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.513A pdb=" N ILE E 124 " --> pdb=" O GLN E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 38 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.795A pdb=" N ASP F 68 " --> pdb=" O SER F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 19 through 23 Processing helix chain 'G' and resid 28 through 39 Processing helix chain 'G' and resid 47 through 50 Processing helix chain 'G' and resid 51 through 57 removed outlier: 3.596A pdb=" N LEU G 57 " --> pdb=" O LEU G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 67 removed outlier: 3.844A pdb=" N LEU G 65 " --> pdb=" O THR G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 74 removed outlier: 4.340A pdb=" N ALA G 71 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA G 72 " --> pdb=" O ALA G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 91 removed outlier: 4.003A pdb=" N LEU G 87 " --> pdb=" O ARG G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 97 removed outlier: 4.413A pdb=" N ASP G 96 " --> pdb=" O ASP G 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 52 removed outlier: 4.405A pdb=" N ILE H 44 " --> pdb=" O TYR H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 84 Processing helix chain 'H' and resid 93 through 104 removed outlier: 4.064A pdb=" N ILE H 97 " --> pdb=" O SER H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 123 Processing sheet with id=AA1, first strand: chain 'K' and resid 170 through 172 removed outlier: 6.759A pdb=" N ILE K 171 " --> pdb=" O ILE K 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 226 through 230 removed outlier: 5.433A pdb=" N GLU K 227 " --> pdb=" O GLU K 238 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU K 238 " --> pdb=" O GLU K 227 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TYR K 229 " --> pdb=" O PHE K 236 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N TYR K 274 " --> pdb=" O TYR K 289 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N TYR K 289 " --> pdb=" O TYR K 274 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET K 276 " --> pdb=" O VAL K 287 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR K 289 " --> pdb=" O LEU K 306 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU K 306 " --> pdb=" O TYR K 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA4, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.420A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 397 hydrogen bonds defined for protein. 1119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 344 hydrogen bonds 680 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 226 stacking parallelities Total time for adding SS restraints: 2.68 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2362 1.32 - 1.44: 6210 1.44 - 1.57: 8667 1.57 - 1.69: 580 1.69 - 1.82: 36 Bond restraints: 17855 Sorted by residual: bond pdb=" N9 DA J 176 " pdb=" C4 DA J 176 " ideal model delta sigma weight residual 1.374 1.317 0.057 6.00e-03 2.78e+04 9.01e+01 bond pdb=" N9 DA I 30 " pdb=" C4 DA I 30 " ideal model delta sigma weight residual 1.374 1.320 0.054 6.00e-03 2.78e+04 8.03e+01 bond pdb=" N9 DA I 29 " pdb=" C4 DA I 29 " ideal model delta sigma weight residual 1.374 1.322 0.052 6.00e-03 2.78e+04 7.42e+01 bond pdb=" C1' DT I 112 " pdb=" N1 DT I 112 " ideal model delta sigma weight residual 1.468 1.352 0.116 1.40e-02 5.10e+03 6.89e+01 bond pdb=" C3' DT J 211 " pdb=" O3' DT J 211 " ideal model delta sigma weight residual 1.435 1.331 0.104 1.30e-02 5.92e+03 6.45e+01 ... (remaining 17850 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 24479 3.58 - 7.16: 758 7.16 - 10.74: 91 10.74 - 14.31: 12 14.31 - 17.89: 7 Bond angle restraints: 25347 Sorted by residual: angle pdb=" O4' DA J 256 " pdb=" C1' DA J 256 " pdb=" N9 DA J 256 " ideal model delta sigma weight residual 108.00 114.46 -6.46 7.00e-01 2.04e+00 8.51e+01 angle pdb=" O5' DG I 81 " pdb=" C5' DG I 81 " pdb=" C4' DG I 81 " ideal model delta sigma weight residual 109.40 115.68 -6.28 8.00e-01 1.56e+00 6.15e+01 angle pdb=" O4' DC J 215 " pdb=" C4' DC J 215 " pdb=" C3' DC J 215 " ideal model delta sigma weight residual 106.00 101.47 4.53 6.00e-01 2.78e+00 5.71e+01 angle pdb=" O4' DT J 183 " pdb=" C4' DT J 183 " pdb=" C3' DT J 183 " ideal model delta sigma weight residual 106.00 101.75 4.25 6.00e-01 2.78e+00 5.02e+01 angle pdb=" CA LEU D 105 " pdb=" C LEU D 105 " pdb=" N PRO D 106 " ideal model delta sigma weight residual 117.59 124.12 -6.53 9.90e-01 1.02e+00 4.35e+01 ... (remaining 25342 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.82: 7792 25.82 - 51.63: 1829 51.63 - 77.45: 468 77.45 - 103.26: 18 103.26 - 129.08: 2 Dihedral angle restraints: 10109 sinusoidal: 6135 harmonic: 3974 Sorted by residual: dihedral pdb=" CA LEU G 57 " pdb=" C LEU G 57 " pdb=" N GLU G 58 " pdb=" CA GLU G 58 " ideal model delta harmonic sigma weight residual -180.00 -128.26 -51.74 0 5.00e+00 4.00e-02 1.07e+02 dihedral pdb=" CA GLN D 59 " pdb=" C GLN D 59 " pdb=" N LYS D 60 " pdb=" CA LYS D 60 " ideal model delta harmonic sigma weight residual 180.00 136.70 43.30 0 5.00e+00 4.00e-02 7.50e+01 dihedral pdb=" CA THR E 80 " pdb=" C THR E 80 " pdb=" N ASP E 81 " pdb=" CA ASP E 81 " ideal model delta harmonic sigma weight residual 180.00 -136.81 -43.19 0 5.00e+00 4.00e-02 7.46e+01 ... (remaining 10106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2472 0.117 - 0.234: 348 0.234 - 0.350: 36 0.350 - 0.467: 1 0.467 - 0.584: 2 Chirality restraints: 2859 Sorted by residual: chirality pdb=" CG LEU E 70 " pdb=" CB LEU E 70 " pdb=" CD1 LEU E 70 " pdb=" CD2 LEU E 70 " both_signs ideal model delta sigma weight residual False -2.59 -2.01 -0.58 2.00e-01 2.50e+01 8.52e+00 chirality pdb=" CG LEU B 97 " pdb=" CB LEU B 97 " pdb=" CD1 LEU B 97 " pdb=" CD2 LEU B 97 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CB ILE C 51 " pdb=" CA ILE C 51 " pdb=" CG1 ILE C 51 " pdb=" CG2 ILE C 51 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.34e+00 ... (remaining 2856 not shown) Planarity restraints: 2191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE K 404 " -0.034 2.00e-02 2.50e+03 2.86e-02 1.43e+01 pdb=" CG PHE K 404 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE K 404 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE K 404 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE K 404 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE K 404 " -0.025 2.00e-02 2.50e+03 pdb=" CZ PHE K 404 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 122 " -0.046 2.00e-02 2.50e+03 2.13e-02 1.36e+01 pdb=" N9 DG I 122 " 0.049 2.00e-02 2.50e+03 pdb=" C8 DG I 122 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 122 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DG I 122 " -0.009 2.00e-02 2.50e+03 pdb=" C6 DG I 122 " 0.010 2.00e-02 2.50e+03 pdb=" O6 DG I 122 " -0.024 2.00e-02 2.50e+03 pdb=" N1 DG I 122 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DG I 122 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG I 122 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG I 122 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DG I 122 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 105 " -0.060 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO H 106 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO H 106 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO H 106 " -0.049 5.00e-02 4.00e+02 ... (remaining 2188 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 2401 2.74 - 3.28: 16737 3.28 - 3.82: 34391 3.82 - 4.36: 38727 4.36 - 4.90: 53808 Nonbonded interactions: 146064 Sorted by model distance: nonbonded pdb=" OG1 THR M 153 " pdb=" OE1 GLU M 155 " model vdw 2.194 3.040 nonbonded pdb=" OG1 THR E 118 " pdb=" O ILE F 46 " model vdw 2.197 3.040 nonbonded pdb=" O ASN N 16 " pdb=" OG SER N 19 " model vdw 2.218 3.040 nonbonded pdb=" O ALA F 33 " pdb=" NH1 ARG F 36 " model vdw 2.224 3.120 nonbonded pdb=" O THR K 356 " pdb=" OG1 THR K 359 " model vdw 2.227 3.040 ... (remaining 146059 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 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 113) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 36 through 128) } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.640 Find NCS groups from input model: 0.130 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5771 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 : 0.013 0.160 17855 Z= 1.094 Angle : 1.543 17.892 25347 Z= 1.071 Chirality : 0.082 0.584 2859 Planarity : 0.009 0.091 2191 Dihedral : 26.157 129.078 7531 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.05 % Favored : 87.95 % Rotamer: Outliers : 2.09 % Allowed : 9.11 % Favored : 88.80 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.89 % Twisted General : 1.93 % 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: -4.82 (0.18), residues: 1320 helix: -3.66 (0.14), residues: 563 sheet: -1.26 (1.49), residues: 14 loop : -2.92 (0.20), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.002 ARG G 21 TYR 0.057 0.005 TYR H 124 PHE 0.060 0.005 PHE K 404 TRP 0.037 0.006 TRP K 353 HIS 0.025 0.004 HIS G 84 Details of bonding type rmsd/Z covalent geometry : bond 0.01271 / 1.09 (17855) covalent geometry : angle 1.54253 / 1.07 (25347) hydrogen bonds : bond 0.22712 / 14.12 ( 741) hydrogen bonds : angle 7.83661 / 5.13 ( 1799) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 373 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 214 TYR cc_start: 0.7639 (t80) cc_final: 0.6991 (t80) REVERT: K 379 MET cc_start: 0.4185 (tpt) cc_final: 0.3299 (tpp) REVERT: K 391 LEU cc_start: 0.9087 (tp) cc_final: 0.8826 (tp) REVERT: M 67 LYS cc_start: 0.6024 (tmmt) cc_final: 0.4809 (mtmm) REVERT: M 68 ILE cc_start: 0.6355 (OUTLIER) cc_final: 0.5726 (tp) REVERT: M 128 MET cc_start: 0.1349 (ptm) cc_final: 0.0967 (ptm) REVERT: M 264 LEU cc_start: 0.2585 (OUTLIER) cc_final: 0.2291 (pp) REVERT: A 85 GLN cc_start: 0.6107 (tm-30) cc_final: 0.5562 (tp40) REVERT: B 50 ILE cc_start: 0.8007 (tp) cc_final: 0.7501 (tp) REVERT: B 55 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.7046 (ptp-170) REVERT: B 68 ASP cc_start: 0.7632 (p0) cc_final: 0.7334 (m-30) REVERT: C 52 TYR cc_start: 0.8085 (t80) cc_final: 0.7757 (t80) REVERT: C 102 THR cc_start: 0.7453 (p) cc_final: 0.7181 (t) REVERT: D 39 THR cc_start: 0.6777 (t) cc_final: 0.5785 (t) REVERT: D 64 ILE cc_start: 0.7014 (OUTLIER) cc_final: 0.6646 (mt) REVERT: D 68 PHE cc_start: 0.6132 (t80) cc_final: 0.5697 (t80) REVERT: D 123 LYS cc_start: 0.7547 (pttp) cc_final: 0.7187 (pttp) REVERT: F 34 ILE cc_start: 0.8731 (tp) cc_final: 0.8525 (tp) REVERT: F 37 LEU cc_start: 0.8113 (mt) cc_final: 0.7709 (mt) REVERT: F 53 GLU cc_start: 0.7978 (pm20) cc_final: 0.7667 (pm20) REVERT: F 58 LEU cc_start: 0.8634 (tt) cc_final: 0.7980 (tp) REVERT: F 61 PHE cc_start: 0.7992 (t80) cc_final: 0.7764 (t80) REVERT: G 35 LEU cc_start: 0.5049 (mp) cc_final: 0.4707 (tp) REVERT: G 87 LEU cc_start: 0.8127 (pp) cc_final: 0.7799 (pp) REVERT: G 110 PRO cc_start: 0.5284 (Cg_endo) cc_final: 0.3756 (Cg_exo) REVERT: H 40 TYR cc_start: 0.6414 (m-10) cc_final: 0.5227 (m-10) REVERT: H 52 HIS cc_start: 0.5764 (m-70) cc_final: 0.5552 (m-70) outliers start: 25 outliers final: 5 residues processed: 386 average time/residue: 0.1490 time to fit residues: 80.8408 Evaluate side-chains 305 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 296 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 9 GLN ** N 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 222 HIS K 250 ASN ** M 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN B 93 GLN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.165003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.143099 restraints weight = 73386.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.145187 restraints weight = 55592.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.146923 restraints weight = 45029.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.148238 restraints weight = 37883.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.148944 restraints weight = 33026.109| |-----------------------------------------------------------------------------| r_work (final): 0.4374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5382 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17855 Z= 0.220 Angle : 1.002 14.425 25347 Z= 0.551 Chirality : 0.059 0.453 2859 Planarity : 0.008 0.115 2191 Dihedral : 30.604 124.325 4760 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 23.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 0.67 % Allowed : 8.53 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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: -4.43 (0.19), residues: 1320 helix: -3.07 (0.16), residues: 603 sheet: -0.40 (1.70), residues: 12 loop : -2.90 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG D 119 TYR 0.065 0.004 TYR M 69 PHE 0.052 0.003 PHE K 404 TRP 0.025 0.003 TRP K 353 HIS 0.014 0.002 HIS G 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.22 (17855) covalent geometry : angle 1.00185 / 0.55 (25347) hydrogen bonds : bond 0.09761 / 6.14 ( 741) hydrogen bonds : angle 6.44039 / 4.26 ( 1799) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 323 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 205 PHE cc_start: 0.5380 (m-10) cc_final: 0.4519 (m-80) REVERT: K 328 SER cc_start: 0.7575 (m) cc_final: 0.7129 (p) REVERT: K 355 ASP cc_start: 0.5610 (p0) cc_final: 0.5360 (p0) REVERT: K 379 MET cc_start: 0.3111 (tpt) cc_final: 0.2601 (tpt) REVERT: K 393 ILE cc_start: 0.7004 (tp) cc_final: 0.6709 (tp) REVERT: K 403 ILE cc_start: 0.7344 (mm) cc_final: 0.7113 (mm) REVERT: M 69 TYR cc_start: 0.5492 (OUTLIER) cc_final: 0.3920 (m-10) REVERT: M 72 ASN cc_start: 0.6602 (t0) cc_final: 0.6168 (t0) REVERT: M 267 LEU cc_start: 0.6541 (pp) cc_final: 0.6264 (pp) REVERT: A 99 TYR cc_start: 0.6547 (m-10) cc_final: 0.6227 (m-80) REVERT: B 39 ARG cc_start: 0.5371 (mmp80) cc_final: 0.5068 (mmp80) REVERT: B 50 ILE cc_start: 0.7900 (tp) cc_final: 0.7632 (tp) REVERT: B 58 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.7116 (mt) REVERT: B 68 ASP cc_start: 0.7567 (p0) cc_final: 0.6575 (m-30) REVERT: D 51 THR cc_start: 0.7069 (p) cc_final: 0.6827 (p) REVERT: D 116 GLU cc_start: 0.7019 (pp20) cc_final: 0.6800 (pp20) REVERT: D 123 LYS cc_start: 0.6785 (pttp) cc_final: 0.6349 (pttm) REVERT: E 104 PHE cc_start: 0.7838 (m-80) cc_final: 0.7378 (m-10) REVERT: F 24 ASP cc_start: 0.7596 (p0) cc_final: 0.7362 (p0) REVERT: F 34 ILE cc_start: 0.8752 (tp) cc_final: 0.8444 (tp) REVERT: F 58 LEU cc_start: 0.8574 (tt) cc_final: 0.7932 (tp) REVERT: F 65 VAL cc_start: 0.7455 (t) cc_final: 0.7018 (p) REVERT: G 86 GLN cc_start: 0.6894 (tp40) cc_final: 0.6495 (mp10) REVERT: H 109 LEU cc_start: 0.7644 (tp) cc_final: 0.7322 (tp) REVERT: H 112 HIS cc_start: 0.6127 (t70) cc_final: 0.5625 (t70) outliers start: 8 outliers final: 2 residues processed: 326 average time/residue: 0.1377 time to fit residues: 63.7951 Evaluate side-chains 268 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 264 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 12 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 114 optimal weight: 0.0970 chunk 132 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 28 optimal weight: 0.0570 chunk 90 optimal weight: 0.8980 chunk 72 optimal weight: 20.0000 chunk 51 optimal weight: 0.4980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 9 GLN N 16 ASN K 222 HIS ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.173537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.152254 restraints weight = 89974.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.153586 restraints weight = 75268.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.154078 restraints weight = 64862.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.154846 restraints weight = 58746.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.156235 restraints weight = 50660.605| |-----------------------------------------------------------------------------| r_work (final): 0.4405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5333 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17855 Z= 0.193 Angle : 0.919 11.971 25347 Z= 0.507 Chirality : 0.055 0.399 2859 Planarity : 0.006 0.056 2191 Dihedral : 30.407 119.229 4760 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 0.33 % Allowed : 7.36 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -4.16 (0.19), residues: 1320 helix: -2.83 (0.16), residues: 614 sheet: -1.49 (1.27), residues: 19 loop : -2.75 (0.21), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 33 TYR 0.053 0.003 TYR B 72 PHE 0.042 0.003 PHE K 404 TRP 0.046 0.003 TRP K 247 HIS 0.009 0.001 HIS G 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.19 (17855) covalent geometry : angle 0.91932 / 0.51 (25347) hydrogen bonds : bond 0.08194 / 5.16 ( 741) hydrogen bonds : angle 5.93484 / 3.95 ( 1799) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 318 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 176 GLU cc_start: 0.8244 (pp20) cc_final: 0.7654 (pp20) REVERT: K 328 SER cc_start: 0.7488 (m) cc_final: 0.6971 (p) REVERT: K 358 ILE cc_start: 0.5389 (pt) cc_final: 0.4725 (pt) REVERT: K 379 MET cc_start: 0.2620 (tpt) cc_final: 0.2136 (tpt) REVERT: K 403 ILE cc_start: 0.7031 (mm) cc_final: 0.6777 (mm) REVERT: M 289 TYR cc_start: 0.5577 (m-80) cc_final: 0.5349 (m-80) REVERT: A 62 ILE cc_start: 0.7105 (mm) cc_final: 0.6586 (mm) REVERT: A 73 GLU cc_start: 0.8050 (tt0) cc_final: 0.7783 (tt0) REVERT: A 99 TYR cc_start: 0.6273 (m-10) cc_final: 0.6005 (m-80) REVERT: B 50 ILE cc_start: 0.7605 (tp) cc_final: 0.7359 (tp) REVERT: B 90 LEU cc_start: 0.6761 (pp) cc_final: 0.6472 (pp) REVERT: E 85 GLN cc_start: 0.4410 (mm-40) cc_final: 0.3969 (mm110) REVERT: E 104 PHE cc_start: 0.7616 (m-80) cc_final: 0.7376 (m-10) REVERT: F 34 ILE cc_start: 0.8800 (tp) cc_final: 0.8430 (tp) REVERT: F 37 LEU cc_start: 0.7939 (mt) cc_final: 0.7692 (mt) REVERT: G 35 LEU cc_start: 0.5353 (tp) cc_final: 0.5112 (tp) REVERT: G 86 GLN cc_start: 0.6799 (tp40) cc_final: 0.6587 (mp10) REVERT: H 66 ASN cc_start: 0.7089 (t0) cc_final: 0.6889 (t0) REVERT: H 112 HIS cc_start: 0.5901 (t70) cc_final: 0.5505 (t70) outliers start: 4 outliers final: 0 residues processed: 319 average time/residue: 0.1329 time to fit residues: 60.2636 Evaluate side-chains 259 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 120 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 135 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 148 optimal weight: 0.0980 chunk 86 optimal weight: 10.0000 chunk 104 optimal weight: 0.0000 chunk 60 optimal weight: 10.0000 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 16 ASN M 163 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 ASN ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.172972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.152811 restraints weight = 90597.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.153527 restraints weight = 84774.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.153796 restraints weight = 75047.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.154378 restraints weight = 69008.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.154579 restraints weight = 61347.295| |-----------------------------------------------------------------------------| r_work (final): 0.4375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5494 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17855 Z= 0.190 Angle : 0.882 13.166 25347 Z= 0.487 Chirality : 0.053 0.378 2859 Planarity : 0.006 0.065 2191 Dihedral : 30.305 117.199 4760 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 22.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.08 % Favored : 89.92 % Rotamer: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.88 (0.20), residues: 1320 helix: -2.54 (0.17), residues: 602 sheet: -1.96 (1.26), residues: 19 loop : -2.65 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 95 TYR 0.051 0.003 TYR K 214 PHE 0.043 0.003 PHE K 404 TRP 0.024 0.004 TRP M 361 HIS 0.013 0.001 HIS G 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.19 (17855) covalent geometry : angle 0.88198 / 0.49 (25347) hydrogen bonds : bond 0.07915 / 5.03 ( 741) hydrogen bonds : angle 5.73590 / 3.83 ( 1799) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 167 LEU cc_start: 0.5639 (tp) cc_final: 0.5396 (tp) REVERT: K 176 GLU cc_start: 0.8313 (pp20) cc_final: 0.7720 (pp20) REVERT: K 316 TYR cc_start: 0.4952 (p90) cc_final: 0.4621 (p90) REVERT: K 403 ILE cc_start: 0.7370 (mm) cc_final: 0.7128 (mm) REVERT: M 289 TYR cc_start: 0.5960 (m-80) cc_final: 0.5630 (m-80) REVERT: A 73 GLU cc_start: 0.8225 (tt0) cc_final: 0.7973 (tt0) REVERT: A 104 PHE cc_start: 0.7658 (m-80) cc_final: 0.7325 (m-80) REVERT: B 90 LEU cc_start: 0.6998 (pp) cc_final: 0.6695 (pp) REVERT: F 37 LEU cc_start: 0.7976 (mt) cc_final: 0.7744 (mt) REVERT: H 66 ASN cc_start: 0.7521 (t0) cc_final: 0.7312 (t0) REVERT: H 112 HIS cc_start: 0.6078 (t70) cc_final: 0.5564 (t70) REVERT: H 122 THR cc_start: 0.8204 (p) cc_final: 0.7989 (p) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.1326 time to fit residues: 58.0577 Evaluate side-chains 257 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 96 optimal weight: 0.6980 chunk 134 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 28 optimal weight: 0.0980 chunk 102 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 16 ASN K 166 ASN B 75 HIS ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.174176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.153894 restraints weight = 90524.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.154421 restraints weight = 76861.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.154650 restraints weight = 74845.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.155695 restraints weight = 65746.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.155926 restraints weight = 58433.637| |-----------------------------------------------------------------------------| r_work (final): 0.4410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5465 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 17855 Z= 0.179 Angle : 0.878 13.516 25347 Z= 0.479 Chirality : 0.053 0.362 2859 Planarity : 0.006 0.076 2191 Dihedral : 30.182 119.009 4760 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.17 % Allowed : 5.77 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.71 (0.20), residues: 1320 helix: -2.36 (0.17), residues: 601 sheet: -1.95 (1.24), residues: 19 loop : -2.60 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 72 TYR 0.045 0.003 TYR D 45 PHE 0.044 0.002 PHE E 104 TRP 0.036 0.003 TRP K 353 HIS 0.015 0.001 HIS G 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.18 (17855) covalent geometry : angle 0.87763 / 0.48 (25347) hydrogen bonds : bond 0.07471 / 4.77 ( 741) hydrogen bonds : angle 5.51385 / 3.65 ( 1799) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 314 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 176 GLU cc_start: 0.8226 (pp20) cc_final: 0.7743 (pp20) REVERT: K 361 LEU cc_start: 0.7982 (mt) cc_final: 0.7685 (mt) REVERT: K 403 ILE cc_start: 0.7259 (mm) cc_final: 0.7038 (mm) REVERT: K 408 ASP cc_start: 0.7101 (p0) cc_final: 0.6405 (p0) REVERT: M 289 TYR cc_start: 0.5926 (m-80) cc_final: 0.5646 (m-80) REVERT: A 61 LEU cc_start: 0.6552 (mp) cc_final: 0.6179 (mp) REVERT: A 62 ILE cc_start: 0.6520 (mt) cc_final: 0.6171 (mm) REVERT: A 73 GLU cc_start: 0.8182 (tt0) cc_final: 0.7963 (tt0) REVERT: A 104 PHE cc_start: 0.7654 (m-80) cc_final: 0.7294 (m-80) REVERT: B 50 ILE cc_start: 0.7891 (tp) cc_final: 0.7648 (tp) REVERT: B 73 THR cc_start: 0.7788 (t) cc_final: 0.7582 (t) REVERT: B 90 LEU cc_start: 0.6902 (pp) cc_final: 0.6647 (pp) REVERT: E 104 PHE cc_start: 0.7567 (m-80) cc_final: 0.7231 (m-80) REVERT: F 24 ASP cc_start: 0.7738 (p0) cc_final: 0.7432 (p0) REVERT: F 58 LEU cc_start: 0.8493 (tp) cc_final: 0.8281 (tp) REVERT: F 80 THR cc_start: 0.5726 (t) cc_final: 0.4612 (t) REVERT: H 66 ASN cc_start: 0.7649 (t0) cc_final: 0.7436 (t0) outliers start: 2 outliers final: 1 residues processed: 315 average time/residue: 0.1387 time to fit residues: 61.6340 Evaluate side-chains 269 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 268 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 46 optimal weight: 0.8980 chunk 87 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 132 optimal weight: 0.2980 chunk 99 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 16 ASN M 163 ASN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 ASN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.173280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.152211 restraints weight = 90103.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.153080 restraints weight = 76785.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.153437 restraints weight = 72081.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.154267 restraints weight = 63691.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.154338 restraints weight = 57038.696| |-----------------------------------------------------------------------------| r_work (final): 0.4395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5554 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17855 Z= 0.193 Angle : 0.881 13.666 25347 Z= 0.482 Chirality : 0.053 0.348 2859 Planarity : 0.006 0.055 2191 Dihedral : 30.061 119.205 4760 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.56 (0.20), residues: 1320 helix: -2.16 (0.18), residues: 603 sheet: -2.40 (1.13), residues: 18 loop : -2.57 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 129 TYR 0.032 0.003 TYR D 86 PHE 0.037 0.002 PHE K 404 TRP 0.029 0.003 TRP K 353 HIS 0.016 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.19 (17855) covalent geometry : angle 0.88136 / 0.48 (25347) hydrogen bonds : bond 0.07598 / 4.85 ( 741) hydrogen bonds : angle 5.40504 / 3.56 ( 1799) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 176 GLU cc_start: 0.8096 (pp20) cc_final: 0.7828 (pp20) REVERT: K 346 LEU cc_start: 0.7897 (mm) cc_final: 0.7476 (mm) REVERT: K 361 LEU cc_start: 0.7847 (mt) cc_final: 0.7637 (mt) REVERT: K 408 ASP cc_start: 0.6917 (p0) cc_final: 0.6330 (p0) REVERT: M 128 MET cc_start: 0.0221 (ptt) cc_final: -0.0044 (ptt) REVERT: M 289 TYR cc_start: 0.6215 (m-80) cc_final: 0.5868 (m-80) REVERT: A 73 GLU cc_start: 0.8194 (tt0) cc_final: 0.7988 (tt0) REVERT: A 104 PHE cc_start: 0.7633 (m-80) cc_final: 0.7208 (m-80) REVERT: B 50 ILE cc_start: 0.7788 (tp) cc_final: 0.7503 (tp) REVERT: B 73 THR cc_start: 0.7389 (t) cc_final: 0.7174 (t) REVERT: C 35 LEU cc_start: 0.8088 (pp) cc_final: 0.7878 (pp) REVERT: D 76 ILE cc_start: 0.8724 (pt) cc_final: 0.8507 (pt) REVERT: D 123 LYS cc_start: 0.7175 (pttp) cc_final: 0.6766 (pttm) REVERT: E 104 PHE cc_start: 0.7639 (m-80) cc_final: 0.7414 (m-10) REVERT: E 126 LEU cc_start: 0.7882 (mm) cc_final: 0.7478 (mm) REVERT: F 24 ASP cc_start: 0.7799 (p0) cc_final: 0.7542 (p0) REVERT: F 34 ILE cc_start: 0.8553 (tp) cc_final: 0.8240 (tp) REVERT: F 37 LEU cc_start: 0.7957 (mt) cc_final: 0.7571 (mt) REVERT: H 66 ASN cc_start: 0.7575 (t0) cc_final: 0.7337 (t0) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.1410 time to fit residues: 61.6561 Evaluate side-chains 262 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 125 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 16 optimal weight: 0.0980 chunk 80 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 16 ASN ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 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 = 0.4653 r_free = 0.4653 target = 0.174385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.151734 restraints weight = 89523.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.152474 restraints weight = 76219.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.153053 restraints weight = 72566.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.154322 restraints weight = 63135.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.154835 restraints weight = 54562.083| |-----------------------------------------------------------------------------| r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5470 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 17855 Z= 0.181 Angle : 0.868 12.707 25347 Z= 0.472 Chirality : 0.052 0.335 2859 Planarity : 0.006 0.095 2191 Dihedral : 29.992 121.402 4760 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.65 (0.20), residues: 1320 helix: -2.23 (0.17), residues: 632 sheet: -2.35 (1.15), residues: 18 loop : -2.62 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG E 72 TYR 0.031 0.003 TYR K 349 PHE 0.034 0.002 PHE K 404 TRP 0.027 0.003 TRP K 353 HIS 0.017 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.18 (17855) covalent geometry : angle 0.86847 / 0.47 (25347) hydrogen bonds : bond 0.07122 / 4.57 ( 741) hydrogen bonds : angle 5.29447 / 3.52 ( 1799) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 87 CYS cc_start: 0.8536 (p) cc_final: 0.8316 (p) REVERT: K 403 ILE cc_start: 0.7284 (mm) cc_final: 0.7084 (mm) REVERT: M 128 MET cc_start: 0.0231 (ptt) cc_final: -0.0069 (ptt) REVERT: M 164 MET cc_start: 0.3461 (ttp) cc_final: 0.3143 (ttp) REVERT: M 289 TYR cc_start: 0.5863 (m-80) cc_final: 0.5639 (m-80) REVERT: A 104 PHE cc_start: 0.7304 (m-80) cc_final: 0.7027 (m-80) REVERT: C 63 GLU cc_start: 0.4183 (pm20) cc_final: 0.3920 (pm20) REVERT: D 72 ILE cc_start: 0.7997 (pt) cc_final: 0.7629 (pt) REVERT: D 103 LEU cc_start: 0.7523 (tp) cc_final: 0.7266 (tp) REVERT: E 104 PHE cc_start: 0.7355 (m-80) cc_final: 0.6981 (m-10) REVERT: F 24 ASP cc_start: 0.7842 (p0) cc_final: 0.7578 (p0) REVERT: F 34 ILE cc_start: 0.8313 (tp) cc_final: 0.8043 (tp) REVERT: F 58 LEU cc_start: 0.8168 (tp) cc_final: 0.7947 (tp) REVERT: H 66 ASN cc_start: 0.7550 (t0) cc_final: 0.7219 (t0) REVERT: H 70 ASN cc_start: 0.7472 (m110) cc_final: 0.7239 (m110) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.1242 time to fit residues: 52.9762 Evaluate side-chains 261 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 121 optimal weight: 2.9990 chunk 6 optimal weight: 0.0060 chunk 27 optimal weight: 3.9990 chunk 130 optimal weight: 0.0050 chunk 150 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 49 optimal weight: 0.0020 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 0.0670 chunk 100 optimal weight: 0.8980 overall best weight: 0.1756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 16 ASN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.175827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.153119 restraints weight = 90853.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.153908 restraints weight = 77459.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.154689 restraints weight = 72081.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.155678 restraints weight = 61682.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.157088 restraints weight = 53994.624| |-----------------------------------------------------------------------------| r_work (final): 0.4427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5370 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 17855 Z= 0.171 Angle : 0.862 11.599 25347 Z= 0.466 Chirality : 0.051 0.319 2859 Planarity : 0.006 0.103 2191 Dihedral : 29.928 122.029 4760 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.49 (0.21), residues: 1320 helix: -2.10 (0.18), residues: 639 sheet: -2.17 (1.25), residues: 19 loop : -2.54 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG D 119 TYR 0.055 0.003 TYR B 72 PHE 0.032 0.002 PHE K 404 TRP 0.034 0.002 TRP K 353 HIS 0.006 0.001 HIS G 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 (17855) covalent geometry : angle 0.86223 / 0.47 (25347) hydrogen bonds : bond 0.06843 / 4.39 ( 741) hydrogen bonds : angle 5.22862 / 3.46 ( 1799) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 35 GLU cc_start: 0.3296 (tm-30) cc_final: 0.2751 (tm-30) REVERT: N 87 CYS cc_start: 0.8529 (p) cc_final: 0.8326 (p) REVERT: K 346 LEU cc_start: 0.7535 (mm) cc_final: 0.7293 (mm) REVERT: K 361 LEU cc_start: 0.7762 (mt) cc_final: 0.7543 (mt) REVERT: K 403 ILE cc_start: 0.7362 (mm) cc_final: 0.7138 (mm) REVERT: M 128 MET cc_start: 0.0074 (ptt) cc_final: -0.0456 (ptt) REVERT: M 229 MET cc_start: 0.3197 (mmm) cc_final: 0.2985 (mmm) REVERT: A 104 PHE cc_start: 0.7236 (m-80) cc_final: 0.7035 (m-80) REVERT: B 90 LEU cc_start: 0.6418 (pp) cc_final: 0.6128 (pp) REVERT: C 97 SER cc_start: 0.6248 (p) cc_final: 0.5727 (p) REVERT: D 103 LEU cc_start: 0.7244 (tp) cc_final: 0.6938 (tp) REVERT: F 24 ASP cc_start: 0.7954 (p0) cc_final: 0.7730 (p0) REVERT: F 34 ILE cc_start: 0.8160 (tp) cc_final: 0.7954 (tp) REVERT: F 37 LEU cc_start: 0.7918 (mt) cc_final: 0.7497 (mt) REVERT: H 66 ASN cc_start: 0.7460 (t0) cc_final: 0.7130 (t0) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.1350 time to fit residues: 56.7292 Evaluate side-chains 258 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 154 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 86 optimal weight: 20.0000 chunk 150 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 16 ASN B 75 HIS ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.172598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.149849 restraints weight = 74021.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.151929 restraints weight = 57794.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.153443 restraints weight = 47648.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.154503 restraints weight = 41029.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.155406 restraints weight = 36679.370| |-----------------------------------------------------------------------------| r_work (final): 0.4399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5428 moved from start: 0.5561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17855 Z= 0.183 Angle : 0.879 12.464 25347 Z= 0.475 Chirality : 0.052 0.329 2859 Planarity : 0.006 0.103 2191 Dihedral : 29.831 120.786 4760 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 21.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.44 (0.21), residues: 1320 helix: -2.01 (0.18), residues: 641 sheet: -3.99 (1.20), residues: 13 loop : -2.53 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 72 TYR 0.043 0.003 TYR B 72 PHE 0.055 0.003 PHE E 104 TRP 0.015 0.003 TRP K 353 HIS 0.008 0.001 HIS G 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 (17855) covalent geometry : angle 0.87852 / 0.48 (25347) hydrogen bonds : bond 0.07105 / 4.57 ( 741) hydrogen bonds : angle 5.20537 / 3.42 ( 1799) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 346 LEU cc_start: 0.8107 (mm) cc_final: 0.7711 (mm) REVERT: K 361 LEU cc_start: 0.7900 (mt) cc_final: 0.7633 (mt) REVERT: K 379 MET cc_start: 0.3546 (tpt) cc_final: 0.3045 (tpt) REVERT: M 128 MET cc_start: 0.0745 (ptt) cc_final: 0.0146 (ptt) REVERT: M 164 MET cc_start: 0.2960 (ttp) cc_final: 0.2596 (ttp) REVERT: M 229 MET cc_start: 0.3215 (mmm) cc_final: 0.2942 (mmm) REVERT: A 104 PHE cc_start: 0.7535 (m-80) cc_final: 0.7140 (m-80) REVERT: B 71 THR cc_start: 0.7956 (p) cc_final: 0.7724 (p) REVERT: B 90 LEU cc_start: 0.6655 (pp) cc_final: 0.6427 (pp) REVERT: D 103 LEU cc_start: 0.7412 (tp) cc_final: 0.7088 (tp) REVERT: E 83 ARG cc_start: 0.7297 (mmp80) cc_final: 0.7078 (mmp80) REVERT: E 103 LEU cc_start: 0.7158 (pp) cc_final: 0.6816 (pp) REVERT: E 104 PHE cc_start: 0.7583 (m-10) cc_final: 0.6828 (t80) REVERT: F 24 ASP cc_start: 0.8067 (p0) cc_final: 0.7853 (p0) REVERT: F 34 ILE cc_start: 0.8407 (tp) cc_final: 0.8111 (tp) REVERT: G 37 ARG cc_start: 0.7096 (ptt-90) cc_final: 0.6873 (mtm110) REVERT: H 38 GLU cc_start: 0.6819 (pm20) cc_final: 0.6583 (pm20) REVERT: H 66 ASN cc_start: 0.7648 (t0) cc_final: 0.7407 (t0) REVERT: H 73 PHE cc_start: 0.6886 (m-10) cc_final: 0.6600 (m-80) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.1423 time to fit residues: 58.9215 Evaluate side-chains 256 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 114 optimal weight: 0.0970 chunk 80 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 40 optimal weight: 0.0470 chunk 11 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 105 optimal weight: 0.5980 chunk 69 optimal weight: 8.9990 chunk 136 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 16 ASN A 113 HIS B 75 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.173719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.151846 restraints weight = 73724.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.154086 restraints weight = 59774.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.155948 restraints weight = 47289.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.156580 restraints weight = 38637.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.156842 restraints weight = 35554.992| |-----------------------------------------------------------------------------| r_work (final): 0.4420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5365 moved from start: 0.5772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 17855 Z= 0.169 Angle : 0.870 11.666 25347 Z= 0.467 Chirality : 0.051 0.300 2859 Planarity : 0.006 0.093 2191 Dihedral : 29.811 121.845 4760 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.39 (0.21), residues: 1320 helix: -1.98 (0.18), residues: 642 sheet: -2.14 (1.26), residues: 18 loop : -2.52 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 72 TYR 0.043 0.003 TYR B 72 PHE 0.074 0.002 PHE E 104 TRP 0.024 0.002 TRP K 353 HIS 0.009 0.001 HIS G 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.17 (17855) covalent geometry : angle 0.87038 / 0.47 (25347) hydrogen bonds : bond 0.06732 / 4.32 ( 741) hydrogen bonds : angle 5.20604 / 3.41 ( 1799) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 35 GLU cc_start: 0.3245 (tm-30) cc_final: 0.2811 (tm-30) REVERT: K 205 PHE cc_start: 0.5047 (m-10) cc_final: 0.4527 (m-10) REVERT: K 346 LEU cc_start: 0.7962 (mm) cc_final: 0.7664 (mm) REVERT: K 361 LEU cc_start: 0.7782 (mt) cc_final: 0.7559 (mt) REVERT: K 403 ILE cc_start: 0.7523 (mm) cc_final: 0.7277 (mm) REVERT: M 128 MET cc_start: 0.0993 (ptt) cc_final: 0.0342 (ptt) REVERT: M 164 MET cc_start: 0.2946 (ttp) cc_final: 0.2588 (ttp) REVERT: M 229 MET cc_start: 0.3037 (mmm) cc_final: 0.2760 (mmm) REVERT: A 104 PHE cc_start: 0.7407 (m-80) cc_final: 0.7139 (m-80) REVERT: B 88 TYR cc_start: 0.6042 (m-10) cc_final: 0.5581 (m-10) REVERT: B 90 LEU cc_start: 0.6479 (pp) cc_final: 0.6245 (pp) REVERT: B 92 ARG cc_start: 0.6124 (mmp-170) cc_final: 0.5600 (mmp80) REVERT: C 97 SER cc_start: 0.6345 (m) cc_final: 0.6128 (p) REVERT: E 65 LEU cc_start: 0.7647 (mt) cc_final: 0.7327 (mt) REVERT: E 83 ARG cc_start: 0.7207 (mmp80) cc_final: 0.6981 (mmp80) REVERT: E 86 SER cc_start: 0.7395 (m) cc_final: 0.7143 (m) REVERT: E 104 PHE cc_start: 0.7583 (m-10) cc_final: 0.6935 (m-10) REVERT: F 24 ASP cc_start: 0.8089 (p0) cc_final: 0.7819 (p0) REVERT: F 34 ILE cc_start: 0.8075 (tp) cc_final: 0.7595 (tp) REVERT: F 37 LEU cc_start: 0.7773 (tp) cc_final: 0.7346 (tp) REVERT: G 37 ARG cc_start: 0.7020 (ptt-90) cc_final: 0.6606 (mtm110) REVERT: H 70 ASN cc_start: 0.7468 (m110) cc_final: 0.7228 (m110) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.1345 time to fit residues: 56.2628 Evaluate side-chains 264 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 128 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 25 optimal weight: 0.1980 chunk 36 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 46 HIS N 16 ASN ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.173371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.151221 restraints weight = 73715.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.153145 restraints weight = 58695.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.154615 restraints weight = 48504.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.155650 restraints weight = 42088.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.156126 restraints weight = 37624.479| |-----------------------------------------------------------------------------| r_work (final): 0.4407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5397 moved from start: 0.5953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17855 Z= 0.167 Angle : 0.869 12.917 25347 Z= 0.467 Chirality : 0.050 0.290 2859 Planarity : 0.006 0.090 2191 Dihedral : 29.742 120.987 4760 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.21), residues: 1320 helix: -1.94 (0.18), residues: 641 sheet: -2.66 (1.14), residues: 19 loop : -2.53 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 67 TYR 0.042 0.003 TYR B 72 PHE 0.050 0.002 PHE E 104 TRP 0.014 0.002 TRP K 353 HIS 0.014 0.001 HIS D 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.17 (17855) covalent geometry : angle 0.86904 / 0.47 (25347) hydrogen bonds : bond 0.06771 / 4.34 ( 741) hydrogen bonds : angle 5.19238 / 3.40 ( 1799) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2448.56 seconds wall clock time: 43 minutes 12.63 seconds (2592.63 seconds total)