Starting phenix.real_space_refine on Sat Jul 4 02:11:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x32_38026/07_2026/8x32_38026.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x32_38026/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8x32_38026/07_2026/8x32_38026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x32_38026/07_2026/8x32_38026.map" model { file = "/net/cci-nas-00/data/ceres_data/8x32_38026/07_2026/8x32_38026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x32_38026/07_2026/8x32_38026.cif" } 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-dev-6108/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: 3.74, per 1000 atoms: 0.22 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: 1.49 Conformation dependent library (CDL) restraints added in 599.1 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: 2.36 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: 3.63 Time building geometry restraints manager: 1.98 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: 24481 3.58 - 7.16: 756 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.580 Find NCS groups from input model: 0.180 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.650 ------------------------------------------------------------------------------- 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= 1.093 Angle : 1.539 17.892 25347 Z= 1.066 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 1.53926 / 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 : 0.500 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: 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: 0.3294 (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: 0.4810 (mtmm) REVERT: M 68 ILE cc_start: 0.6355 (OUTLIER) cc_final: 0.5723 (tp) REVERT: M 128 MET cc_start: 0.1349 (ptm) cc_final: 0.0966 (ptm) REVERT: M 264 LEU cc_start: 0.2585 (OUTLIER) cc_final: 0.2289 (pp) REVERT: A 85 GLN cc_start: 0.6107 (tm-30) cc_final: 0.5446 (tp40) REVERT: A 118 THR cc_start: 0.7325 (m) cc_final: 0.6985 (m) REVERT: B 50 ILE cc_start: 0.8007 (tp) cc_final: 0.7499 (tp) REVERT: B 55 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.7048 (ptp-170) REVERT: B 68 ASP cc_start: 0.7632 (p0) cc_final: 0.7333 (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: 0.7192 (t) REVERT: D 39 THR cc_start: 0.6777 (t) cc_final: 0.6145 (t) REVERT: D 64 ILE cc_start: 0.7014 (OUTLIER) cc_final: 0.6641 (mt) REVERT: D 68 PHE cc_start: 0.6132 (t80) cc_final: 0.5689 (t80) REVERT: D 123 LYS cc_start: 0.7547 (pttp) cc_final: 0.7188 (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: 0.7711 (mt) REVERT: F 53 GLU cc_start: 0.7978 (pm20) cc_final: 0.7665 (pm20) REVERT: F 58 LEU cc_start: 0.8634 (tt) cc_final: 0.7979 (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: 0.7801 (pp) REVERT: G 110 PRO cc_start: 0.5284 (Cg_endo) cc_final: 0.3737 (Cg_exo) REVERT: H 40 TYR cc_start: 0.6414 (m-10) cc_final: 0.5226 (m-10) REVERT: H 52 HIS cc_start: 0.5764 (m-70) cc_final: 0.5556 (m-70) outliers start: 25 outliers final: 5 residues processed: 386 average time/residue: 0.1783 time to fit residues: 95.7938 Evaluate side-chains 306 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 297 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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: 0.0870 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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 = 0.4584 r_free = 0.4584 target = 0.165730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.144152 restraints weight = 74346.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.146405 restraints weight = 56965.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.147627 restraints weight = 46307.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.148881 restraints weight = 39805.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.149989 restraints weight = 33504.916| |-----------------------------------------------------------------------------| r_work (final): 0.4387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5330 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17855 Z= 0.214 Angle : 0.984 14.109 25347 Z= 0.540 Chirality : 0.057 0.436 2859 Planarity : 0.008 0.106 2191 Dihedral : 30.669 123.133 4760 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 0.75 % Allowed : 8.28 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -4.40 (0.19), residues: 1320 helix: -3.01 (0.16), residues: 602 sheet: -0.41 (1.70), residues: 12 loop : -2.93 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 395 TYR 0.041 0.003 TYR K 311 PHE 0.050 0.003 PHE K 404 TRP 0.027 0.003 TRP K 353 HIS 0.015 0.002 HIS G 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.21 (17855) covalent geometry : angle 0.98402 / 0.54 (25347) hydrogen bonds : bond 0.09269 / 5.88 ( 741) hydrogen bonds : angle 6.33405 / 4.20 ( 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: 9 poor density : 322 time to evaluate : 0.433 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: K 205 PHE cc_start: 0.5348 (m-10) cc_final: 0.4369 (m-80) REVERT: K 328 SER cc_start: 0.7582 (m) cc_final: 0.7109 (p) REVERT: K 329 LYS cc_start: 0.7411 (mtmm) cc_final: 0.7201 (mtmm) REVERT: K 379 MET cc_start: 0.2612 (tpt) cc_final: 0.2190 (tpt) REVERT: K 393 ILE cc_start: 0.6999 (tp) cc_final: 0.6716 (tp) REVERT: K 403 ILE cc_start: 0.7273 (mm) cc_final: 0.7040 (mm) REVERT: M 69 TYR cc_start: 0.5526 (OUTLIER) cc_final: 0.3887 (m-10) REVERT: M 72 ASN cc_start: 0.6602 (t0) cc_final: 0.6083 (t0) REVERT: M 200 ILE cc_start: 0.6279 (mp) cc_final: 0.6079 (mp) REVERT: A 62 ILE cc_start: 0.7531 (mm) cc_final: 0.7137 (mm) REVERT: A 99 TYR cc_start: 0.6461 (m-10) cc_final: 0.6177 (m-80) REVERT: A 118 THR cc_start: 0.6683 (m) cc_final: 0.6424 (m) REVERT: B 39 ARG cc_start: 0.5220 (mmp80) cc_final: 0.4934 (mmp80) REVERT: B 50 ILE cc_start: 0.7830 (tp) cc_final: 0.7552 (tp) REVERT: B 58 LEU cc_start: 0.7364 (mm) cc_final: 0.7104 (mt) REVERT: B 68 ASP cc_start: 0.7617 (p0) cc_final: 0.6638 (m-30) REVERT: D 87 ASN cc_start: 0.7767 (p0) cc_final: 0.7539 (p0) REVERT: D 122 THR cc_start: 0.8309 (p) cc_final: 0.8107 (p) REVERT: E 104 PHE cc_start: 0.7867 (m-80) cc_final: 0.7258 (m-10) REVERT: F 34 ILE cc_start: 0.8739 (tp) cc_final: 0.8294 (tp) REVERT: F 58 LEU cc_start: 0.8483 (tt) cc_final: 0.7833 (tt) REVERT: F 65 VAL cc_start: 0.7405 (t) cc_final: 0.6977 (p) REVERT: G 35 LEU cc_start: 0.4824 (mp) cc_final: 0.4523 (tp) REVERT: H 112 HIS cc_start: 0.6096 (t70) cc_final: 0.5594 (t70) outliers start: 9 outliers final: 2 residues processed: 328 average time/residue: 0.1563 time to fit residues: 72.4278 Evaluate side-chains 266 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 263 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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: 1.9990 chunk 93 optimal weight: 0.8980 chunk 143 optimal weight: 0.5980 chunk 49 optimal weight: 0.3980 chunk 114 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 72 optimal weight: 20.0000 chunk 51 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 16 ASN K 222 HIS ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** 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 = 0.4632 r_free = 0.4632 target = 0.173084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.151300 restraints weight = 90009.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.152666 restraints weight = 74390.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.153142 restraints weight = 67764.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.154257 restraints weight = 57950.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.154381 restraints weight = 50905.115| |-----------------------------------------------------------------------------| r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5400 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17855 Z= 0.191 Angle : 0.898 11.591 25347 Z= 0.496 Chirality : 0.055 0.368 2859 Planarity : 0.007 0.151 2191 Dihedral : 30.449 118.709 4760 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 20.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 0.25 % Allowed : 6.77 % Favored : 92.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -4.15 (0.20), residues: 1320 helix: -2.77 (0.17), residues: 615 sheet: -1.53 (1.26), residues: 19 loop : -2.79 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 30 TYR 0.046 0.003 TYR B 72 PHE 0.042 0.003 PHE K 404 TRP 0.040 0.004 TRP K 247 HIS 0.013 0.001 HIS G 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.19 (17855) covalent geometry : angle 0.89831 / 0.50 (25347) hydrogen bonds : bond 0.08369 / 5.30 ( 741) hydrogen bonds : angle 5.93353 / 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 317 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 314 time to evaluate : 0.514 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: K 176 GLU cc_start: 0.8283 (pp20) cc_final: 0.7666 (pp20) REVERT: K 215 ARG cc_start: 0.7332 (tpt90) cc_final: 0.6971 (tpt90) REVERT: K 328 SER cc_start: 0.7449 (m) cc_final: 0.6900 (p) REVERT: K 379 MET cc_start: 0.2461 (tpt) cc_final: 0.2043 (tpt) REVERT: K 403 ILE cc_start: 0.7037 (mm) cc_final: 0.6792 (mm) REVERT: M 72 ASN cc_start: 0.6529 (t0) cc_final: 0.6256 (t0) REVERT: M 289 TYR cc_start: 0.5768 (m-80) cc_final: 0.5467 (m-80) REVERT: A 62 ILE cc_start: 0.7135 (mm) cc_final: 0.6554 (mm) REVERT: A 99 TYR cc_start: 0.6344 (m-10) cc_final: 0.6118 (m-80) REVERT: A 118 THR cc_start: 0.6077 (m) cc_final: 0.5799 (m) REVERT: B 37 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7139 (pp) REVERT: B 90 LEU cc_start: 0.6913 (pp) cc_final: 0.6586 (pp) REVERT: D 76 ILE cc_start: 0.8243 (pt) cc_final: 0.8042 (pt) REVERT: D 116 GLU cc_start: 0.7286 (pp20) cc_final: 0.7012 (pp20) REVERT: D 123 LYS cc_start: 0.7147 (pttp) cc_final: 0.6638 (pttm) REVERT: E 104 PHE cc_start: 0.7635 (m-80) cc_final: 0.7345 (m-10) REVERT: F 34 ILE cc_start: 0.8789 (tp) cc_final: 0.8365 (tp) REVERT: F 37 LEU cc_start: 0.7934 (mt) cc_final: 0.7661 (mt) REVERT: G 35 LEU cc_start: 0.4926 (mp) cc_final: 0.4622 (tp) REVERT: H 70 ASN cc_start: 0.7474 (m110) cc_final: 0.7266 (m110) REVERT: H 112 HIS cc_start: 0.5964 (t70) cc_final: 0.5540 (t70) outliers start: 3 outliers final: 0 residues processed: 316 average time/residue: 0.1666 time to fit residues: 74.4635 Evaluate side-chains 267 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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: 1.9990 chunk 78 optimal weight: 9.9990 chunk 135 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 148 optimal weight: 0.4980 chunk 86 optimal weight: 10.0000 chunk 104 optimal weight: 0.0170 chunk 60 optimal weight: 9.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 16 ASN A 68 GLN D 59 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.173361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.153816 restraints weight = 90905.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.153992 restraints weight = 81807.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.154260 restraints weight = 78130.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.155127 restraints weight = 69722.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.155090 restraints weight = 62547.479| |-----------------------------------------------------------------------------| r_work (final): 0.4380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5503 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17855 Z= 0.176 Angle : 0.870 14.136 25347 Z= 0.479 Chirality : 0.053 0.349 2859 Planarity : 0.006 0.072 2191 Dihedral : 30.349 119.634 4760 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 0.08 % Allowed : 5.77 % Favored : 94.15 % 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: -3.84 (0.20), residues: 1320 helix: -2.46 (0.17), residues: 608 sheet: -2.01 (1.01), residues: 29 loop : -2.67 (0.22), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 95 TYR 0.059 0.003 TYR K 214 PHE 0.039 0.003 PHE K 404 TRP 0.025 0.003 TRP K 247 HIS 0.018 0.001 HIS G 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.18 (17855) covalent geometry : angle 0.86950 / 0.48 (25347) hydrogen bonds : bond 0.07619 / 4.85 ( 741) hydrogen bonds : angle 5.66112 / 3.76 ( 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 311 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 310 time to evaluate : 0.490 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: K 176 GLU cc_start: 0.8306 (pp20) cc_final: 0.7730 (pp20) REVERT: K 328 SER cc_start: 0.7625 (m) cc_final: 0.7151 (p) REVERT: M 72 ASN cc_start: 0.6608 (t0) cc_final: 0.6321 (t0) REVERT: M 252 GLN cc_start: 0.6316 (mm-40) cc_final: 0.5990 (mm-40) REVERT: M 289 TYR cc_start: 0.5892 (m-80) cc_final: 0.5575 (m-80) REVERT: A 104 PHE cc_start: 0.7682 (m-80) cc_final: 0.7287 (m-80) REVERT: B 68 ASP cc_start: 0.7656 (m-30) cc_final: 0.7428 (m-30) REVERT: B 73 THR cc_start: 0.7444 (t) cc_final: 0.6937 (t) REVERT: D 87 ASN cc_start: 0.7970 (p0) cc_final: 0.7752 (p0) REVERT: D 119 ARG cc_start: 0.7483 (ttp80) cc_final: 0.7268 (ttp80) REVERT: E 104 PHE cc_start: 0.7633 (m-80) cc_final: 0.7410 (m-10) REVERT: F 37 LEU cc_start: 0.8112 (mt) cc_final: 0.7894 (mt) REVERT: F 78 ARG cc_start: 0.7630 (mmm160) cc_final: 0.7278 (mmm-85) REVERT: G 35 LEU cc_start: 0.4896 (mp) cc_final: 0.4522 (tp) REVERT: H 38 GLU cc_start: 0.6970 (pm20) cc_final: 0.6709 (pm20) REVERT: H 109 LEU cc_start: 0.7509 (tp) cc_final: 0.7251 (tt) REVERT: H 112 HIS cc_start: 0.6201 (t70) cc_final: 0.5640 (t70) outliers start: 1 outliers final: 0 residues processed: 310 average time/residue: 0.1658 time to fit residues: 72.7602 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 : 0.493 ------------------------------------------------------------------------------- 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: 5.9990 chunk 134 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 116 optimal weight: 0.6980 chunk 22 optimal weight: 0.0470 chunk 90 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 102 optimal weight: 0.5980 chunk 83 optimal weight: 10.0000 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 16 ASN K 166 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS ** 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 = 0.4653 r_free = 0.4653 target = 0.174430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.152491 restraints weight = 90005.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.153322 restraints weight = 75163.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.153860 restraints weight = 71931.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.154835 restraints weight = 60216.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.155126 restraints weight = 55250.994| |-----------------------------------------------------------------------------| r_work (final): 0.4390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5495 moved from start: 0.4406 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 : 0.849 12.855 25347 Z= 0.466 Chirality : 0.052 0.336 2859 Planarity : 0.006 0.104 2191 Dihedral : 30.249 119.922 4760 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 0.08 % Allowed : 5.02 % Favored : 94.90 % 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: -3.68 (0.20), residues: 1320 helix: -2.33 (0.17), residues: 611 sheet: -1.76 (1.20), residues: 19 loop : -2.59 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 83 TYR 0.037 0.003 TYR A 99 PHE 0.041 0.002 PHE K 404 TRP 0.036 0.003 TRP K 353 HIS 0.018 0.001 HIS G 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.17 (17855) covalent geometry : angle 0.84931 / 0.47 (25347) hydrogen bonds : bond 0.07278 / 4.64 ( 741) hydrogen bonds : angle 5.43009 / 3.60 ( 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 308 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 307 time to evaluate : 0.495 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: K 176 GLU cc_start: 0.8200 (pp20) cc_final: 0.7658 (pp20) REVERT: K 328 SER cc_start: 0.7591 (m) cc_final: 0.7134 (p) REVERT: K 361 LEU cc_start: 0.7862 (mt) cc_final: 0.7651 (mt) REVERT: K 403 ILE cc_start: 0.7338 (mm) cc_final: 0.7122 (mm) REVERT: K 408 ASP cc_start: 0.7084 (p0) cc_final: 0.6435 (p0) REVERT: M 72 ASN cc_start: 0.6527 (t0) cc_final: 0.6263 (t0) REVERT: M 289 TYR cc_start: 0.5974 (m-80) cc_final: 0.5625 (m-80) REVERT: A 99 TYR cc_start: 0.6357 (m-80) cc_final: 0.6144 (m-80) REVERT: A 109 LEU cc_start: 0.8307 (mt) cc_final: 0.8033 (tp) REVERT: B 50 ILE cc_start: 0.7612 (tp) cc_final: 0.7406 (tp) REVERT: B 73 THR cc_start: 0.7340 (t) cc_final: 0.7015 (t) REVERT: D 87 ASN cc_start: 0.7899 (p0) cc_final: 0.7596 (p0) REVERT: D 103 LEU cc_start: 0.7507 (tp) cc_final: 0.7242 (tp) REVERT: E 104 PHE cc_start: 0.7536 (m-80) cc_final: 0.7251 (m-10) REVERT: F 24 ASP cc_start: 0.7526 (p0) cc_final: 0.7198 (p0) REVERT: F 34 ILE cc_start: 0.8499 (tp) cc_final: 0.8187 (tp) REVERT: F 37 LEU cc_start: 0.8029 (mt) cc_final: 0.7738 (mt) REVERT: F 61 PHE cc_start: 0.7744 (t80) cc_final: 0.7538 (t80) REVERT: H 73 PHE cc_start: 0.7047 (m-10) cc_final: 0.6662 (m-10) REVERT: H 112 HIS cc_start: 0.6176 (t70) cc_final: 0.5644 (t70) outliers start: 1 outliers final: 0 residues processed: 308 average time/residue: 0.1729 time to fit residues: 74.8151 Evaluate side-chains 255 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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: 0.7980 chunk 87 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 16 ASN K 365 GLN B 75 HIS D 70 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.172511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.151506 restraints weight = 76634.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.153274 restraints weight = 62806.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.154065 restraints weight = 53672.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.155887 restraints weight = 46529.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.156169 restraints weight = 39394.073| |-----------------------------------------------------------------------------| r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5355 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17855 Z= 0.179 Angle : 0.859 12.490 25347 Z= 0.470 Chirality : 0.052 0.320 2859 Planarity : 0.006 0.089 2191 Dihedral : 30.144 120.148 4760 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -3.70 (0.20), residues: 1320 helix: -2.22 (0.18), residues: 633 sheet: -2.07 (1.01), residues: 28 loop : -2.71 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 55 TYR 0.040 0.003 TYR B 72 PHE 0.036 0.002 PHE K 404 TRP 0.032 0.003 TRP K 353 HIS 0.012 0.001 HIS G 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.18 (17855) covalent geometry : angle 0.85868 / 0.47 (25347) hydrogen bonds : bond 0.07311 / 4.67 ( 741) hydrogen bonds : angle 5.32295 / 3.52 ( 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 301 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.493 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: N 86 LYS cc_start: 0.4554 (tptt) cc_final: 0.3985 (tptt) REVERT: K 361 LEU cc_start: 0.7655 (mt) cc_final: 0.7425 (mt) REVERT: K 403 ILE cc_start: 0.7415 (mm) cc_final: 0.7030 (mm) REVERT: M 128 MET cc_start: 0.0489 (ptt) cc_final: 0.0164 (ptt) REVERT: B 74 GLU cc_start: 0.4094 (mp0) cc_final: 0.3773 (mp0) REVERT: B 90 LEU cc_start: 0.6708 (pp) cc_final: 0.6462 (pp) REVERT: D 76 ILE cc_start: 0.8651 (pt) cc_final: 0.8382 (pt) REVERT: D 103 LEU cc_start: 0.7377 (tp) cc_final: 0.7108 (tp) REVERT: F 24 ASP cc_start: 0.7577 (p0) cc_final: 0.7307 (p0) REVERT: F 34 ILE cc_start: 0.8479 (tp) cc_final: 0.8180 (tp) REVERT: F 37 LEU cc_start: 0.8060 (mt) cc_final: 0.7799 (mt) REVERT: F 61 PHE cc_start: 0.7796 (t80) cc_final: 0.7464 (t80) REVERT: H 73 PHE cc_start: 0.6985 (m-10) cc_final: 0.6732 (m-10) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.1774 time to fit residues: 74.3442 Evaluate side-chains 253 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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: 1.9990 chunk 5 optimal weight: 0.5980 chunk 136 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 16 ASN K 168 ASN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.173136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.151325 restraints weight = 89470.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.152197 restraints weight = 77255.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.152764 restraints weight = 72161.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.153542 restraints weight = 63110.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.153818 restraints weight = 55707.616| |-----------------------------------------------------------------------------| r_work (final): 0.4380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5587 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17855 Z= 0.207 Angle : 0.882 12.703 25347 Z= 0.486 Chirality : 0.053 0.308 2859 Planarity : 0.007 0.071 2191 Dihedral : 30.035 121.012 4760 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 23.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -3.57 (0.20), residues: 1320 helix: -2.11 (0.18), residues: 630 sheet: -2.29 (1.24), residues: 18 loop : -2.64 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 44 TYR 0.030 0.003 TYR K 349 PHE 0.048 0.003 PHE E 104 TRP 0.029 0.003 TRP K 353 HIS 0.021 0.002 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.21 (17855) covalent geometry : angle 0.88236 / 0.49 (25347) hydrogen bonds : bond 0.07614 / 4.87 ( 741) hydrogen bonds : angle 5.40783 / 3.59 ( 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 290 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.521 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: M 128 MET cc_start: 0.0293 (ptt) cc_final: -0.0005 (ptt) REVERT: M 164 MET cc_start: 0.3453 (ttp) cc_final: 0.2846 (ttp) REVERT: B 73 THR cc_start: 0.7633 (t) cc_final: 0.7407 (t) REVERT: E 104 PHE cc_start: 0.7719 (m-10) cc_final: 0.7399 (m-10) REVERT: F 24 ASP cc_start: 0.7961 (p0) cc_final: 0.7709 (p0) REVERT: F 34 ILE cc_start: 0.8501 (tp) cc_final: 0.8172 (tp) REVERT: F 37 LEU cc_start: 0.7912 (mt) cc_final: 0.7683 (mt) REVERT: G 97 SER cc_start: 0.6916 (t) cc_final: 0.6708 (t) REVERT: H 73 PHE cc_start: 0.7110 (m-10) cc_final: 0.6856 (m-10) REVERT: H 108 GLU cc_start: 0.6962 (pp20) cc_final: 0.6754 (pm20) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.1761 time to fit residues: 71.6108 Evaluate side-chains 249 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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: 0.2980 chunk 6 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 130 optimal weight: 0.0000 chunk 150 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 16 ASN ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 365 GLN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.172952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.150229 restraints weight = 72772.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.152591 restraints weight = 56873.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.153687 restraints weight = 47040.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.155042 restraints weight = 41169.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.156325 restraints weight = 34592.690| |-----------------------------------------------------------------------------| r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5404 moved from start: 0.5367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 17855 Z= 0.175 Angle : 0.865 13.013 25347 Z= 0.469 Chirality : 0.052 0.308 2859 Planarity : 0.006 0.052 2191 Dihedral : 30.037 124.120 4760 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -3.57 (0.21), residues: 1320 helix: -2.18 (0.18), residues: 645 sheet: -2.13 (1.01), residues: 28 loop : -2.55 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 119 TYR 0.042 0.003 TYR B 72 PHE 0.044 0.002 PHE E 104 TRP 0.034 0.003 TRP K 353 HIS 0.026 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (17855) covalent geometry : angle 0.86532 / 0.47 (25347) hydrogen bonds : bond 0.06945 / 4.44 ( 741) hydrogen bonds : angle 5.29252 / 3.49 ( 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 291 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.500 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: 0.3320 (tm-30) cc_final: 0.2857 (tm-30) REVERT: K 361 LEU cc_start: 0.7918 (mt) cc_final: 0.7658 (mt) REVERT: K 403 ILE cc_start: 0.7559 (mm) cc_final: 0.7130 (mp) REVERT: M 128 MET cc_start: 0.0423 (ptt) cc_final: -0.0243 (ptt) REVERT: M 164 MET cc_start: 0.3185 (ttp) cc_final: 0.2575 (ttp) REVERT: M 166 GLU cc_start: 0.6628 (tp30) cc_final: 0.6344 (tp30) REVERT: M 229 MET cc_start: 0.3242 (mmm) cc_final: 0.3013 (mmm) REVERT: B 90 LEU cc_start: 0.6757 (pp) cc_final: 0.6466 (pp) REVERT: D 72 ILE cc_start: 0.7975 (pt) cc_final: 0.7659 (pt) REVERT: E 100 LEU cc_start: 0.7695 (pp) cc_final: 0.7431 (pp) REVERT: E 104 PHE cc_start: 0.7623 (m-10) cc_final: 0.7412 (m-10) REVERT: F 24 ASP cc_start: 0.7974 (p0) cc_final: 0.7752 (p0) REVERT: F 34 ILE cc_start: 0.8436 (tp) cc_final: 0.8032 (tp) REVERT: F 58 LEU cc_start: 0.8084 (tp) cc_final: 0.7844 (mt) REVERT: H 108 GLU cc_start: 0.7221 (pp20) cc_final: 0.6787 (pm20) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.1742 time to fit residues: 70.8032 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 : 0.373 ------------------------------------------------------------------------------- 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: 0.9980 chunk 122 optimal weight: 0.8980 chunk 86 optimal weight: 20.0000 chunk 150 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 16 ASN ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 168 ASN ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.172352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.149879 restraints weight = 73635.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.151913 restraints weight = 57911.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.153359 restraints weight = 47883.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.154532 restraints weight = 41492.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.155205 restraints weight = 37007.740| |-----------------------------------------------------------------------------| r_work (final): 0.4395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5421 moved from start: 0.5597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 17855 Z= 0.179 Angle : 0.870 12.402 25347 Z= 0.473 Chirality : 0.051 0.279 2859 Planarity : 0.006 0.064 2191 Dihedral : 29.941 123.896 4760 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 21.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % 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 : 0.23 % 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: -3.56 (0.20), residues: 1320 helix: -2.16 (0.17), residues: 641 sheet: -3.20 (1.06), residues: 22 loop : -2.52 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 21 TYR 0.044 0.003 TYR D 124 PHE 0.042 0.002 PHE K 404 TRP 0.030 0.003 TRP K 353 HIS 0.024 0.002 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.18 (17855) covalent geometry : angle 0.86982 / 0.47 (25347) hydrogen bonds : bond 0.07068 / 4.52 ( 741) hydrogen bonds : angle 5.26373 / 3.48 ( 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 287 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.500 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: L 35 GLU cc_start: 0.3353 (tm-30) cc_final: 0.2620 (tm-30) REVERT: K 361 LEU cc_start: 0.7885 (mt) cc_final: 0.7598 (mt) REVERT: M 128 MET cc_start: 0.0390 (ptt) cc_final: -0.0118 (ptt) REVERT: M 166 GLU cc_start: 0.6694 (tp30) cc_final: 0.6324 (tp30) REVERT: M 229 MET cc_start: 0.3432 (mmm) cc_final: 0.3149 (mmm) REVERT: A 104 PHE cc_start: 0.7391 (m-80) cc_final: 0.7024 (m-80) REVERT: B 68 ASP cc_start: 0.7787 (m-30) cc_final: 0.7064 (m-30) REVERT: B 90 LEU cc_start: 0.6683 (pp) cc_final: 0.6444 (pp) REVERT: B 92 ARG cc_start: 0.6290 (mmp80) cc_final: 0.5865 (mmp80) REVERT: C 19 SER cc_start: 0.7200 (p) cc_final: 0.6716 (m) REVERT: D 76 ILE cc_start: 0.8618 (pt) cc_final: 0.8376 (pt) REVERT: E 72 ARG cc_start: 0.5790 (tpt170) cc_final: 0.5537 (tpt170) REVERT: E 100 LEU cc_start: 0.7704 (pp) cc_final: 0.7464 (pp) REVERT: E 104 PHE cc_start: 0.7574 (m-10) cc_final: 0.7250 (m-10) REVERT: F 34 ILE cc_start: 0.8415 (tp) cc_final: 0.8026 (tp) REVERT: F 58 LEU cc_start: 0.8070 (tp) cc_final: 0.7802 (mt) REVERT: H 108 GLU cc_start: 0.7283 (pp20) cc_final: 0.6881 (pm20) REVERT: H 112 HIS cc_start: 0.5857 (m-70) cc_final: 0.5640 (m-70) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.1739 time to fit residues: 69.9439 Evaluate side-chains 249 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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: 0.0980 chunk 80 optimal weight: 9.9990 chunk 43 optimal weight: 0.7980 chunk 40 optimal weight: 0.0770 chunk 11 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 105 optimal weight: 0.0570 chunk 69 optimal weight: 10.0000 chunk 136 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 46 HIS N 16 ASN ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 168 ASN ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.173605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.151120 restraints weight = 74100.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.153440 restraints weight = 60514.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.154557 restraints weight = 49461.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.155954 restraints weight = 41278.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.156114 restraints weight = 37259.350| |-----------------------------------------------------------------------------| r_work (final): 0.4412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5398 moved from start: 0.5841 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= 0.170 Angle : 0.866 13.201 25347 Z= 0.467 Chirality : 0.051 0.260 2859 Planarity : 0.006 0.080 2191 Dihedral : 29.909 125.097 4760 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: -2.13 (0.18), residues: 642 sheet: -2.22 (0.98), residues: 28 loop : -2.50 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 67 TYR 0.038 0.003 TYR K 311 PHE 0.035 0.002 PHE E 104 TRP 0.028 0.002 TRP K 353 HIS 0.022 0.002 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.17 (17855) covalent geometry : angle 0.86629 / 0.47 (25347) hydrogen bonds : bond 0.06765 / 4.32 ( 741) hydrogen bonds : angle 5.23123 / 3.47 ( 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 291 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.392 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: L 35 GLU cc_start: 0.3273 (tm-30) cc_final: 0.2673 (tm-30) REVERT: K 403 ILE cc_start: 0.7589 (mm) cc_final: 0.7150 (mp) REVERT: M 128 MET cc_start: 0.0808 (ptt) cc_final: 0.0181 (ptt) REVERT: M 166 GLU cc_start: 0.6563 (tp30) cc_final: 0.6307 (tp30) REVERT: M 229 MET cc_start: 0.3118 (mmm) cc_final: 0.2858 (mmm) REVERT: A 104 PHE cc_start: 0.7380 (m-80) cc_final: 0.7064 (m-80) REVERT: B 68 ASP cc_start: 0.7807 (m-30) cc_final: 0.7040 (m-30) REVERT: B 90 LEU cc_start: 0.6517 (pp) cc_final: 0.6219 (pp) REVERT: F 34 ILE cc_start: 0.8353 (tp) cc_final: 0.8052 (tp) REVERT: F 58 LEU cc_start: 0.7995 (tp) cc_final: 0.7594 (mt) REVERT: F 77 LYS cc_start: 0.5969 (mmmt) cc_final: 0.5748 (mmmt) REVERT: H 109 LEU cc_start: 0.7625 (tp) cc_final: 0.7354 (tp) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.1731 time to fit residues: 70.5645 Evaluate side-chains 247 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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: 0.5980 chunk 51 optimal weight: 0.0030 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 27 optimal weight: 0.5980 chunk 61 optimal weight: 10.0000 chunk 25 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 0.0980 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 16 ASN ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** 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 = 0.4656 r_free = 0.4656 target = 0.174254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.151822 restraints weight = 74626.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.153820 restraints weight = 59932.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.154674 restraints weight = 51034.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.156319 restraints weight = 45198.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.156756 restraints weight = 38501.732| |-----------------------------------------------------------------------------| r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5393 moved from start: 0.6010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17855 Z= 0.167 Angle : 0.866 13.584 25347 Z= 0.469 Chirality : 0.051 0.260 2859 Planarity : 0.006 0.073 2191 Dihedral : 29.859 124.861 4760 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % 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 : 0.31 % 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: -3.47 (0.21), residues: 1320 helix: -2.08 (0.18), residues: 639 sheet: -2.46 (0.98), residues: 29 loop : -2.51 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 67 TYR 0.041 0.003 TYR K 311 PHE 0.054 0.002 PHE E 104 TRP 0.034 0.003 TRP K 353 HIS 0.022 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.17 (17855) covalent geometry : angle 0.86611 / 0.47 (25347) hydrogen bonds : bond 0.06770 / 4.34 ( 741) hydrogen bonds : angle 5.17128 / 3.41 ( 1799) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3050.42 seconds wall clock time: 53 minutes 49.59 seconds (3229.59 seconds total)