Starting phenix.real_space_refine on Thu Sep 18 09:50:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c5a_45209/09_2025/9c5a_45209.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c5a_45209/09_2025/9c5a_45209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9c5a_45209/09_2025/9c5a_45209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c5a_45209/09_2025/9c5a_45209.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c5a_45209/09_2025/9c5a_45209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c5a_45209/09_2025/9c5a_45209.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 68 5.16 5 C 10114 2.51 5 N 2688 2.21 5 O 2928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15806 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain breaks: 2 Chain: "M" Number of atoms: 3309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3309 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 391} Chain: "C" Number of atoms: 1447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1447 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 3, 'TRANS': 176} Chain: "Y" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 62 Classifications: {'peptide': 8} Modifications used: {'COO': 1} Link IDs: {'TRANS': 7} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: b, m, c, y Time building chain proxies: 4.45, per 1000 atoms: 0.28 Number of scatterers: 15806 At special positions: 0 Unit cell: (92.046, 189.382, 93.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 68 16.00 P 6 15.00 Mg 2 11.99 O 2928 8.00 N 2688 7.00 C 10114 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: 1.37 Conformation dependent library (CDL) restraints added in 673.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3772 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 14 sheets defined 50.8% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 55 through 72 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 79 through 84 Processing helix chain 'B' and resid 85 through 89 removed outlier: 3.656A pdb=" N ALA B 88 " --> pdb=" O LYS B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 106 Processing helix chain 'B' and resid 109 through 115 Processing helix chain 'B' and resid 117 through 124 Processing helix chain 'B' and resid 128 through 141 Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 147 through 160 Processing helix chain 'B' and resid 163 through 181 Processing helix chain 'B' and resid 184 through 197 removed outlier: 3.520A pdb=" N LYS B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 215 removed outlier: 5.001A pdb=" N SER B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 224 removed outlier: 4.219A pdb=" N HIS B 223 " --> pdb=" O ASP B 220 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LYS B 224 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 233 Processing helix chain 'B' and resid 237 through 256 removed outlier: 3.532A pdb=" N VAL B 243 " --> pdb=" O TRP B 239 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 305 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 312 through 327 Processing helix chain 'B' and resid 328 through 334 removed outlier: 4.939A pdb=" N GLY B 333 " --> pdb=" O SER B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 343 removed outlier: 3.764A pdb=" N LEU B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 362 removed outlier: 3.772A pdb=" N ILE B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 376 removed outlier: 6.429A pdb=" N GLY B 366 " --> pdb=" O GLN B 363 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU B 369 " --> pdb=" O GLY B 366 " (cutoff:3.500A) Proline residue: B 370 - end of helix removed outlier: 5.747A pdb=" N LYS B 373 " --> pdb=" O PRO B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 397 Processing helix chain 'B' and resid 401 through 415 removed outlier: 4.263A pdb=" N ARG B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 621 through 627 Processing helix chain 'B' and resid 645 through 649 Processing helix chain 'M' and resid 25 through 27 No H-bonds generated for 'chain 'M' and resid 25 through 27' Processing helix chain 'M' and resid 28 through 38 removed outlier: 4.143A pdb=" N PHE M 32 " --> pdb=" O VAL M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 45 removed outlier: 4.044A pdb=" N VAL M 45 " --> pdb=" O VAL M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 95 Processing helix chain 'M' and resid 98 through 116 removed outlier: 6.454A pdb=" N VAL M 107 " --> pdb=" O LYS M 103 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE M 108 " --> pdb=" O ASP M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 134 removed outlier: 4.600A pdb=" N GLU M 132 " --> pdb=" O ASN M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 138 through 149 removed outlier: 3.526A pdb=" N ILE M 147 " --> pdb=" O VAL M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 163 Processing helix chain 'M' and resid 224 through 226 No H-bonds generated for 'chain 'M' and resid 224 through 226' Processing helix chain 'M' and resid 238 through 245 removed outlier: 3.625A pdb=" N TRP M 242 " --> pdb=" O ARG M 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 13 Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'C' and resid 74 through 82 Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 135 through 144 Processing helix chain 'C' and resid 145 through 148 Processing helix chain 'C' and resid 165 through 178 Processing helix chain 'b' and resid 41 through 53 Processing helix chain 'b' and resid 55 through 72 Processing helix chain 'b' and resid 76 through 78 No H-bonds generated for 'chain 'b' and resid 76 through 78' Processing helix chain 'b' and resid 79 through 84 Processing helix chain 'b' and resid 85 through 89 removed outlier: 3.657A pdb=" N ALA b 88 " --> pdb=" O LYS b 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 106 Processing helix chain 'b' and resid 109 through 115 Processing helix chain 'b' and resid 117 through 124 Processing helix chain 'b' and resid 128 through 141 Processing helix chain 'b' and resid 144 through 146 No H-bonds generated for 'chain 'b' and resid 144 through 146' Processing helix chain 'b' and resid 147 through 160 Processing helix chain 'b' and resid 163 through 181 Processing helix chain 'b' and resid 184 through 197 removed outlier: 3.521A pdb=" N LYS b 197 " --> pdb=" O GLU b 193 " (cutoff:3.500A) Processing helix chain 'b' and resid 200 through 215 removed outlier: 5.002A pdb=" N SER b 206 " --> pdb=" O LEU b 202 " (cutoff:3.500A) Processing helix chain 'b' and resid 218 through 224 removed outlier: 4.217A pdb=" N HIS b 223 " --> pdb=" O ASP b 220 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS b 224 " --> pdb=" O LEU b 221 " (cutoff:3.500A) Processing helix chain 'b' and resid 225 through 233 Processing helix chain 'b' and resid 237 through 256 removed outlier: 3.530A pdb=" N VAL b 243 " --> pdb=" O TRP b 239 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR b 254 " --> pdb=" O ARG b 250 " (cutoff:3.500A) Processing helix chain 'b' and resid 296 through 305 Processing helix chain 'b' and resid 306 through 310 Processing helix chain 'b' and resid 312 through 327 Processing helix chain 'b' and resid 328 through 334 removed outlier: 4.939A pdb=" N GLY b 333 " --> pdb=" O SER b 330 " (cutoff:3.500A) Processing helix chain 'b' and resid 335 through 343 removed outlier: 3.764A pdb=" N LEU b 343 " --> pdb=" O LEU b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 362 removed outlier: 3.771A pdb=" N ILE b 362 " --> pdb=" O ALA b 358 " (cutoff:3.500A) Processing helix chain 'b' and resid 363 through 376 removed outlier: 6.430A pdb=" N GLY b 366 " --> pdb=" O GLN b 363 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU b 369 " --> pdb=" O GLY b 366 " (cutoff:3.500A) Proline residue: b 370 - end of helix removed outlier: 5.748A pdb=" N LYS b 373 " --> pdb=" O PRO b 370 " (cutoff:3.500A) Processing helix chain 'b' and resid 382 through 397 Processing helix chain 'b' and resid 401 through 415 removed outlier: 4.263A pdb=" N ARG b 407 " --> pdb=" O SER b 403 " (cutoff:3.500A) Processing helix chain 'b' and resid 417 through 427 Processing helix chain 'b' and resid 621 through 627 Processing helix chain 'b' and resid 645 through 649 Processing helix chain 'm' and resid 25 through 27 No H-bonds generated for 'chain 'm' and resid 25 through 27' Processing helix chain 'm' and resid 28 through 38 removed outlier: 4.143A pdb=" N PHE m 32 " --> pdb=" O VAL m 28 " (cutoff:3.500A) Processing helix chain 'm' and resid 41 through 45 removed outlier: 4.043A pdb=" N VAL m 45 " --> pdb=" O VAL m 42 " (cutoff:3.500A) Processing helix chain 'm' and resid 75 through 95 Processing helix chain 'm' and resid 98 through 116 removed outlier: 6.454A pdb=" N VAL m 107 " --> pdb=" O LYS m 103 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE m 108 " --> pdb=" O ASP m 104 " (cutoff:3.500A) Processing helix chain 'm' and resid 126 through 134 removed outlier: 4.600A pdb=" N GLU m 132 " --> pdb=" O ASN m 128 " (cutoff:3.500A) Processing helix chain 'm' and resid 138 through 149 removed outlier: 3.527A pdb=" N ILE m 147 " --> pdb=" O VAL m 143 " (cutoff:3.500A) Processing helix chain 'm' and resid 158 through 163 Processing helix chain 'm' and resid 224 through 226 No H-bonds generated for 'chain 'm' and resid 224 through 226' Processing helix chain 'm' and resid 238 through 245 removed outlier: 3.626A pdb=" N TRP m 242 " --> pdb=" O ARG m 238 " (cutoff:3.500A) Processing helix chain 'c' and resid 3 through 13 Processing helix chain 'c' and resid 29 through 39 Processing helix chain 'c' and resid 74 through 82 Processing helix chain 'c' and resid 96 through 98 No H-bonds generated for 'chain 'c' and resid 96 through 98' Processing helix chain 'c' and resid 99 through 112 Processing helix chain 'c' and resid 113 through 117 Processing helix chain 'c' and resid 135 through 144 Processing helix chain 'c' and resid 145 through 148 Processing helix chain 'c' and resid 165 through 178 Processing sheet with id=AA1, first strand: chain 'M' and resid 14 through 19 removed outlier: 5.845A pdb=" N ILE M 14 " --> pdb=" O ASN M 9 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASN M 9 " --> pdb=" O ILE M 14 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER M 4 " --> pdb=" O VAL M 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 117 through 118 Processing sheet with id=AA3, first strand: chain 'M' and resid 228 through 233 removed outlier: 3.861A pdb=" N ASP M 230 " --> pdb=" O ARG M 263 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ASN M 256 " --> pdb=" O ILE M 210 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE M 210 " --> pdb=" O ASN M 256 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ARG M 258 " --> pdb=" O ALA M 208 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA M 208 " --> pdb=" O ARG M 258 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE M 202 " --> pdb=" O VAL M 264 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA M 179 " --> pdb=" O LYS M 403 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL M 405 " --> pdb=" O ALA M 179 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE M 181 " --> pdb=" O VAL M 405 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N TYR M 407 " --> pdb=" O PHE M 181 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL M 183 " --> pdb=" O TYR M 407 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N THR M 409 " --> pdb=" O VAL M 183 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU M 185 " --> pdb=" O THR M 409 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ALA M 411 " --> pdb=" O GLU M 185 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ILE M 187 " --> pdb=" O ALA M 411 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS M 413 " --> pdb=" O ILE M 187 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N PHE M 377 " --> pdb=" O ALA M 411 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LYS M 413 " --> pdb=" O ILE M 375 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE M 375 " --> pdb=" O LYS M 413 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN M 415 " --> pdb=" O LEU M 373 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU M 373 " --> pdb=" O GLN M 415 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN M 374 " --> pdb=" O VAL M 310 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL M 310 " --> pdb=" O ASN M 374 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN M 376 " --> pdb=" O ILE M 308 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE M 308 " --> pdb=" O GLN M 376 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLU M 306 " --> pdb=" O LYS M 345 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LYS M 345 " --> pdb=" O GLU M 306 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ILE M 308 " --> pdb=" O VAL M 343 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 228 through 233 removed outlier: 3.861A pdb=" N ASP M 230 " --> pdb=" O ARG M 263 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ASN M 256 " --> pdb=" O ILE M 210 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE M 210 " --> pdb=" O ASN M 256 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ARG M 258 " --> pdb=" O ALA M 208 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA M 208 " --> pdb=" O ARG M 258 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE M 202 " --> pdb=" O VAL M 264 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA M 179 " --> pdb=" O LYS M 403 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL M 405 " --> pdb=" O ALA M 179 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE M 181 " --> pdb=" O VAL M 405 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N TYR M 407 " --> pdb=" O PHE M 181 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL M 183 " --> pdb=" O TYR M 407 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N THR M 409 " --> pdb=" O VAL M 183 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU M 185 " --> pdb=" O THR M 409 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ALA M 411 " --> pdb=" O GLU M 185 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ILE M 187 " --> pdb=" O ALA M 411 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS M 413 " --> pdb=" O ILE M 187 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 248 through 250 removed outlier: 6.415A pdb=" N SER M 219 " --> pdb=" O LEU M 392 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU M 392 " --> pdb=" O SER M 219 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N SER M 221 " --> pdb=" O ASN M 390 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 274 through 281 removed outlier: 6.257A pdb=" N SER M 353 " --> pdb=" O PRO M 325 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LYS M 355 " --> pdb=" O LEU M 323 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LEU M 323 " --> pdb=" O LYS M 355 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU M 357 " --> pdb=" O MET M 321 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N MET M 321 " --> pdb=" O LEU M 357 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN M 359 " --> pdb=" O LEU M 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 51 through 58 removed outlier: 4.913A pdb=" N GLY C 24 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N GLY C 87 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ARG C 19 " --> pdb=" O GLY C 87 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ILE C 89 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU C 21 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL C 91 " --> pdb=" O LEU C 21 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL C 23 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N ASP C 93 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU C 121 " --> pdb=" O TYR C 154 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLN C 156 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL C 123 " --> pdb=" O GLN C 156 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'm' and resid 14 through 19 removed outlier: 5.845A pdb=" N ILE m 14 " --> pdb=" O ASN m 9 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASN m 9 " --> pdb=" O ILE m 14 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER m 4 " --> pdb=" O VAL m 69 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'm' and resid 117 through 118 Processing sheet with id=AB1, first strand: chain 'm' and resid 228 through 233 removed outlier: 3.860A pdb=" N ASP m 230 " --> pdb=" O ARG m 263 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASN m 256 " --> pdb=" O ILE m 210 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ILE m 210 " --> pdb=" O ASN m 256 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ARG m 258 " --> pdb=" O ALA m 208 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA m 208 " --> pdb=" O ARG m 258 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE m 202 " --> pdb=" O VAL m 264 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA m 179 " --> pdb=" O LYS m 403 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL m 405 " --> pdb=" O ALA m 179 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE m 181 " --> pdb=" O VAL m 405 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N TYR m 407 " --> pdb=" O PHE m 181 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL m 183 " --> pdb=" O TYR m 407 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N THR m 409 " --> pdb=" O VAL m 183 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLU m 185 " --> pdb=" O THR m 409 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ALA m 411 " --> pdb=" O GLU m 185 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ILE m 187 " --> pdb=" O ALA m 411 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS m 413 " --> pdb=" O ILE m 187 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N PHE m 377 " --> pdb=" O ALA m 411 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LYS m 413 " --> pdb=" O ILE m 375 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE m 375 " --> pdb=" O LYS m 413 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN m 415 " --> pdb=" O LEU m 373 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU m 373 " --> pdb=" O GLN m 415 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN m 374 " --> pdb=" O VAL m 310 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL m 310 " --> pdb=" O ASN m 374 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLN m 376 " --> pdb=" O ILE m 308 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE m 308 " --> pdb=" O GLN m 376 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLU m 306 " --> pdb=" O LYS m 345 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LYS m 345 " --> pdb=" O GLU m 306 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ILE m 308 " --> pdb=" O VAL m 343 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'm' and resid 228 through 233 removed outlier: 3.860A pdb=" N ASP m 230 " --> pdb=" O ARG m 263 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASN m 256 " --> pdb=" O ILE m 210 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ILE m 210 " --> pdb=" O ASN m 256 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ARG m 258 " --> pdb=" O ALA m 208 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA m 208 " --> pdb=" O ARG m 258 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE m 202 " --> pdb=" O VAL m 264 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA m 179 " --> pdb=" O LYS m 403 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL m 405 " --> pdb=" O ALA m 179 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE m 181 " --> pdb=" O VAL m 405 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N TYR m 407 " --> pdb=" O PHE m 181 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL m 183 " --> pdb=" O TYR m 407 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N THR m 409 " --> pdb=" O VAL m 183 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLU m 185 " --> pdb=" O THR m 409 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ALA m 411 " --> pdb=" O GLU m 185 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ILE m 187 " --> pdb=" O ALA m 411 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS m 413 " --> pdb=" O ILE m 187 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'm' and resid 248 through 250 removed outlier: 6.415A pdb=" N SER m 219 " --> pdb=" O LEU m 392 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU m 392 " --> pdb=" O SER m 219 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N SER m 221 " --> pdb=" O ASN m 390 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'm' and resid 274 through 281 removed outlier: 6.258A pdb=" N SER m 353 " --> pdb=" O PRO m 325 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LYS m 355 " --> pdb=" O LEU m 323 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LEU m 323 " --> pdb=" O LYS m 355 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU m 357 " --> pdb=" O MET m 321 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N MET m 321 " --> pdb=" O LEU m 357 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN m 359 " --> pdb=" O LEU m 319 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 51 through 58 removed outlier: 4.913A pdb=" N GLY c 24 " --> pdb=" O VAL c 68 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N GLY c 87 " --> pdb=" O GLU c 17 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG c 19 " --> pdb=" O GLY c 87 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE c 89 " --> pdb=" O ARG c 19 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU c 21 " --> pdb=" O ILE c 89 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL c 91 " --> pdb=" O LEU c 21 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL c 23 " --> pdb=" O VAL c 91 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N ASP c 93 " --> pdb=" O VAL c 23 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU c 121 " --> pdb=" O TYR c 154 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLN c 156 " --> pdb=" O LEU c 121 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL c 123 " --> pdb=" O GLN c 156 " (cutoff:3.500A) 865 hydrogen bonds defined for protein. 2361 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3578 1.32 - 1.44: 3570 1.44 - 1.57: 8832 1.57 - 1.69: 10 1.69 - 1.81: 118 Bond restraints: 16108 Sorted by residual: bond pdb=" CA ILE b 174 " pdb=" C ILE b 174 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.22e-02 6.72e+03 1.38e+01 bond pdb=" CA ILE B 174 " pdb=" C ILE B 174 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.22e-02 6.72e+03 1.38e+01 bond pdb=" CA ARG b 132 " pdb=" C ARG b 132 " ideal model delta sigma weight residual 1.524 1.477 0.047 1.27e-02 6.20e+03 1.35e+01 bond pdb=" CA ARG B 132 " pdb=" C ARG B 132 " ideal model delta sigma weight residual 1.524 1.477 0.047 1.27e-02 6.20e+03 1.34e+01 bond pdb=" CA ASN M 105 " pdb=" CB ASN M 105 " ideal model delta sigma weight residual 1.528 1.481 0.047 1.35e-02 5.49e+03 1.19e+01 ... (remaining 16103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 19347 2.14 - 4.28: 2064 4.28 - 6.42: 297 6.42 - 8.56: 92 8.56 - 10.69: 22 Bond angle restraints: 21822 Sorted by residual: angle pdb=" C ASP b 181 " pdb=" N PRO b 182 " pdb=" CA PRO b 182 " ideal model delta sigma weight residual 119.56 129.06 -9.50 1.02e+00 9.61e-01 8.67e+01 angle pdb=" C ASP B 181 " pdb=" N PRO B 182 " pdb=" CA PRO B 182 " ideal model delta sigma weight residual 119.56 129.03 -9.47 1.02e+00 9.61e-01 8.62e+01 angle pdb=" C ASP B 645 " pdb=" N PRO B 646 " pdb=" CA PRO B 646 " ideal model delta sigma weight residual 119.56 129.00 -9.44 1.02e+00 9.61e-01 8.57e+01 angle pdb=" C ASP b 645 " pdb=" N PRO b 646 " pdb=" CA PRO b 646 " ideal model delta sigma weight residual 119.56 128.94 -9.38 1.02e+00 9.61e-01 8.47e+01 angle pdb=" C LEU c 130 " pdb=" N PRO c 131 " pdb=" CA PRO c 131 " ideal model delta sigma weight residual 119.56 128.46 -8.90 1.02e+00 9.61e-01 7.61e+01 ... (remaining 21817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 9702 35.81 - 71.61: 108 71.61 - 107.42: 18 107.42 - 143.22: 4 143.22 - 179.03: 4 Dihedral angle restraints: 9836 sinusoidal: 4034 harmonic: 5802 Sorted by residual: dihedral pdb=" O3B GTP c1001 " pdb=" O3A GTP c1001 " pdb=" PB GTP c1001 " pdb=" PA GTP c1001 " ideal model delta sinusoidal sigma weight residual -68.92 110.10 -179.03 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O3B GTP C1001 " pdb=" O3A GTP C1001 " pdb=" PB GTP C1001 " pdb=" PA GTP C1001 " ideal model delta sinusoidal sigma weight residual -68.92 110.06 -178.98 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C8 GTP C1001 " pdb=" C1' GTP C1001 " pdb=" N9 GTP C1001 " pdb=" O4' GTP C1001 " ideal model delta sinusoidal sigma weight residual 104.59 -70.81 175.40 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 9833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1373 0.054 - 0.109: 836 0.109 - 0.163: 254 0.163 - 0.217: 53 0.217 - 0.271: 8 Chirality restraints: 2524 Sorted by residual: chirality pdb=" CA LYS m 21 " pdb=" N LYS m 21 " pdb=" C LYS m 21 " pdb=" CB LYS m 21 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA LYS M 21 " pdb=" N LYS M 21 " pdb=" C LYS M 21 " pdb=" CB LYS M 21 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA SER B 118 " pdb=" N SER B 118 " pdb=" C SER B 118 " pdb=" CB SER B 118 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2521 not shown) Planarity restraints: 2752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE y 417 " -0.028 2.00e-02 2.50e+03 5.69e-02 3.24e+01 pdb=" C ILE y 417 " 0.098 2.00e-02 2.50e+03 pdb=" O ILE y 417 " -0.035 2.00e-02 2.50e+03 pdb=" OXT ILE y 417 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE Y 417 " 0.028 2.00e-02 2.50e+03 5.68e-02 3.23e+01 pdb=" C ILE Y 417 " -0.098 2.00e-02 2.50e+03 pdb=" O ILE Y 417 " 0.035 2.00e-02 2.50e+03 pdb=" OXT ILE Y 417 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 275 " 0.033 2.00e-02 2.50e+03 1.74e-02 6.09e+00 pdb=" CG TYR M 275 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR M 275 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR M 275 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR M 275 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR M 275 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR M 275 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR M 275 " 0.024 2.00e-02 2.50e+03 ... (remaining 2749 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 51 2.49 - 3.09: 12930 3.09 - 3.69: 24298 3.69 - 4.30: 37073 4.30 - 4.90: 58123 Nonbonded interactions: 132475 Sorted by model distance: nonbonded pdb=" OG1 THR c 31 " pdb="MG MG c1000 " model vdw 1.887 2.170 nonbonded pdb=" OG1 THR C 31 " pdb="MG MG C1000 " model vdw 1.887 2.170 nonbonded pdb="MG MG C1000 " pdb=" O2G GTP C1001 " model vdw 1.940 2.170 nonbonded pdb="MG MG c1000 " pdb=" O2G GTP c1001 " model vdw 1.940 2.170 nonbonded pdb=" O ARG b 344 " pdb=" NH1 ARG b 344 " model vdw 2.158 3.120 ... (remaining 132470 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: 0.03 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'Y' selection = chain 'y' } 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: 4.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.920 Find NCS groups from input model: 0.120 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 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 : 0.014 0.064 16108 Z= 0.907 Angle : 1.485 10.695 21822 Z= 1.030 Chirality : 0.073 0.271 2524 Planarity : 0.005 0.057 2752 Dihedral : 12.262 179.025 6064 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.53 % Favored : 96.32 % Rotamer: Outliers : 0.45 % Allowed : 0.00 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.19), residues: 1954 helix: -0.39 (0.16), residues: 814 sheet: 0.07 (0.26), residues: 356 loop : 1.10 (0.24), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 132 TYR 0.033 0.005 TYR M 275 PHE 0.025 0.004 PHE C 124 TRP 0.025 0.005 TRP C 153 HIS 0.008 0.002 HIS b 624 Details of bonding type rmsd covalent geometry : bond 0.01406 (16108) covalent geometry : angle 1.48497 (21822) hydrogen bonds : bond 0.17054 ( 815) hydrogen bonds : angle 7.97942 ( 2361) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 828 time to evaluate : 0.479 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: B 43 LYS cc_start: 0.8347 (mttt) cc_final: 0.7774 (mmmt) REVERT: B 50 MET cc_start: 0.8532 (mtm) cc_final: 0.8140 (mpp) REVERT: B 51 LEU cc_start: 0.8621 (mt) cc_final: 0.8294 (mt) REVERT: B 54 ASN cc_start: 0.7812 (p0) cc_final: 0.7578 (t0) REVERT: B 55 LYS cc_start: 0.8314 (ttpt) cc_final: 0.8015 (mtpt) REVERT: B 59 LYS cc_start: 0.8531 (mttm) cc_final: 0.8262 (mttp) REVERT: B 63 MET cc_start: 0.8436 (mmm) cc_final: 0.8059 (mmm) REVERT: B 64 LYS cc_start: 0.9111 (mttt) cc_final: 0.8690 (mtpp) REVERT: B 72 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8579 (mtmt) REVERT: B 74 LYS cc_start: 0.8508 (mmtt) cc_final: 0.8237 (mmtt) REVERT: B 83 VAL cc_start: 0.8651 (t) cc_final: 0.8447 (t) REVERT: B 85 LYS cc_start: 0.8733 (mttt) cc_final: 0.8344 (mttt) REVERT: B 89 SER cc_start: 0.8248 (t) cc_final: 0.8011 (t) REVERT: B 91 ASN cc_start: 0.6673 (t0) cc_final: 0.5815 (t0) REVERT: B 94 ILE cc_start: 0.8327 (mt) cc_final: 0.8091 (mt) REVERT: B 97 LEU cc_start: 0.8836 (mt) cc_final: 0.8405 (mm) REVERT: B 101 TYR cc_start: 0.8557 (t80) cc_final: 0.8257 (t80) REVERT: B 120 PHE cc_start: 0.8398 (m-80) cc_final: 0.8090 (m-10) REVERT: B 121 GLN cc_start: 0.8390 (tt0) cc_final: 0.8162 (mt0) REVERT: B 125 LYS cc_start: 0.8703 (mttt) cc_final: 0.8365 (mtpp) REVERT: B 132 ARG cc_start: 0.8451 (mtt180) cc_final: 0.8132 (ttm170) REVERT: B 137 ARG cc_start: 0.7881 (mtp-110) cc_final: 0.7656 (mtp-110) REVERT: B 141 SER cc_start: 0.8461 (m) cc_final: 0.8008 (t) REVERT: B 165 TYR cc_start: 0.8540 (t80) cc_final: 0.8272 (t80) REVERT: B 175 GLN cc_start: 0.8324 (tm-30) cc_final: 0.8009 (tm-30) REVERT: B 177 LEU cc_start: 0.8597 (tp) cc_final: 0.8296 (tp) REVERT: B 181 ASP cc_start: 0.8067 (t0) cc_final: 0.7742 (t0) REVERT: B 185 LYS cc_start: 0.7854 (tttt) cc_final: 0.7288 (ttpp) REVERT: B 190 GLU cc_start: 0.8063 (tt0) cc_final: 0.7116 (tt0) REVERT: B 191 VAL cc_start: 0.8990 (t) cc_final: 0.8222 (t) REVERT: B 194 LYS cc_start: 0.8887 (mttt) cc_final: 0.8319 (mttt) REVERT: B 196 LEU cc_start: 0.8478 (mt) cc_final: 0.8163 (tp) REVERT: B 215 CYS cc_start: 0.7816 (t) cc_final: 0.7122 (t) REVERT: B 226 TYR cc_start: 0.7785 (t80) cc_final: 0.7572 (t80) REVERT: B 241 GLN cc_start: 0.8461 (mt0) cc_final: 0.7636 (mt0) REVERT: B 244 ILE cc_start: 0.9113 (mt) cc_final: 0.8686 (tp) REVERT: B 246 HIS cc_start: 0.8442 (m-70) cc_final: 0.7724 (m-70) REVERT: B 247 MET cc_start: 0.7401 (tmm) cc_final: 0.7077 (tmm) REVERT: B 298 ARG cc_start: 0.8335 (mmm160) cc_final: 0.7966 (mpt180) REVERT: B 305 LYS cc_start: 0.9012 (tttt) cc_final: 0.8797 (ttpp) REVERT: B 311 ARG cc_start: 0.8182 (ptt180) cc_final: 0.7702 (ptt-90) REVERT: B 317 MET cc_start: 0.8603 (tpp) cc_final: 0.8298 (tpt) REVERT: B 324 TRP cc_start: 0.8683 (t-100) cc_final: 0.8415 (t-100) REVERT: B 326 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7795 (mm) REVERT: B 341 ARG cc_start: 0.8771 (ptt90) cc_final: 0.7908 (ttp-110) REVERT: B 417 ASP cc_start: 0.8032 (t0) cc_final: 0.7538 (m-30) REVERT: B 635 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7475 (mt-10) REVERT: B 640 PRO cc_start: 0.8755 (Cg_exo) cc_final: 0.8374 (Cg_endo) REVERT: B 641 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8169 (pm20) REVERT: M 15 PHE cc_start: 0.7944 (t80) cc_final: 0.7681 (t80) REVERT: M 16 LEU cc_start: 0.8681 (tt) cc_final: 0.8384 (tp) REVERT: M 17 GLU cc_start: 0.7704 (pt0) cc_final: 0.7463 (pt0) REVERT: M 21 LYS cc_start: 0.8513 (mttt) cc_final: 0.7786 (mttp) REVERT: M 30 ASP cc_start: 0.8314 (m-30) cc_final: 0.7975 (t0) REVERT: M 33 PHE cc_start: 0.8449 (m-80) cc_final: 0.8101 (m-80) REVERT: M 34 GLU cc_start: 0.8900 (tt0) cc_final: 0.8527 (tt0) REVERT: M 36 GLN cc_start: 0.8486 (tp40) cc_final: 0.8264 (tp40) REVERT: M 43 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7412 (mt-10) REVERT: M 44 ASN cc_start: 0.8121 (t0) cc_final: 0.7509 (t0) REVERT: M 60 TYR cc_start: 0.8409 (t80) cc_final: 0.8180 (t80) REVERT: M 78 PHE cc_start: 0.9077 (t80) cc_final: 0.8805 (t80) REVERT: M 81 GLU cc_start: 0.7360 (tp30) cc_final: 0.6821 (tp30) REVERT: M 108 ILE cc_start: 0.8854 (mt) cc_final: 0.8638 (mt) REVERT: M 115 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7775 (tp30) REVERT: M 116 MET cc_start: 0.7833 (mtm) cc_final: 0.7265 (mtm) REVERT: M 119 ASN cc_start: 0.8320 (t0) cc_final: 0.7520 (t0) REVERT: M 126 GLU cc_start: 0.8076 (tp30) cc_final: 0.7785 (tp30) REVERT: M 134 ILE cc_start: 0.8158 (mt) cc_final: 0.7495 (mt) REVERT: M 135 LYS cc_start: 0.8700 (mmtt) cc_final: 0.8207 (mmtt) REVERT: M 157 LEU cc_start: 0.8353 (mt) cc_final: 0.8084 (mt) REVERT: M 159 THR cc_start: 0.8251 (m) cc_final: 0.7984 (t) REVERT: M 173 LYS cc_start: 0.7479 (tttt) cc_final: 0.7155 (tttt) REVERT: M 181 PHE cc_start: 0.8115 (m-80) cc_final: 0.7592 (m-80) REVERT: M 182 ASP cc_start: 0.6599 (m-30) cc_final: 0.6068 (m-30) REVERT: M 183 VAL cc_start: 0.8071 (t) cc_final: 0.7672 (p) REVERT: M 203 GLN cc_start: 0.7374 (mm-40) cc_final: 0.7045 (mm-40) REVERT: M 209 CYS cc_start: 0.7655 (t) cc_final: 0.6590 (m) REVERT: M 220 LEU cc_start: 0.8202 (mt) cc_final: 0.7988 (mt) REVERT: M 227 LEU cc_start: 0.8905 (mt) cc_final: 0.8594 (mp) REVERT: M 240 LYS cc_start: 0.8411 (mttt) cc_final: 0.8006 (mttt) REVERT: M 252 PRO cc_start: 0.8677 (Cg_endo) cc_final: 0.8433 (Cg_exo) REVERT: M 257 PHE cc_start: 0.8283 (p90) cc_final: 0.8061 (p90) REVERT: M 258 ARG cc_start: 0.8221 (mtm180) cc_final: 0.7957 (mtm-85) REVERT: M 259 LEU cc_start: 0.8660 (tp) cc_final: 0.8353 (tp) REVERT: M 298 LYS cc_start: 0.8303 (tttt) cc_final: 0.7952 (tttt) REVERT: M 299 GLN cc_start: 0.7408 (mt0) cc_final: 0.5853 (mt0) REVERT: M 300 ASN cc_start: 0.8434 (p0) cc_final: 0.8056 (p0) REVERT: M 414 PHE cc_start: 0.7647 (t80) cc_final: 0.7103 (t80) REVERT: C 22 MET cc_start: 0.7581 (ttm) cc_final: 0.6876 (ttm) REVERT: C 39 LEU cc_start: 0.8509 (mt) cc_final: 0.8248 (mt) REVERT: C 45 THR cc_start: 0.8728 (p) cc_final: 0.8421 (t) REVERT: C 64 THR cc_start: 0.7108 (m) cc_final: 0.6575 (t) REVERT: C 68 VAL cc_start: 0.8500 (t) cc_final: 0.8107 (p) REVERT: C 81 TYR cc_start: 0.7067 (m-80) cc_final: 0.6220 (m-80) REVERT: C 82 PHE cc_start: 0.8163 (m-10) cc_final: 0.7730 (m-80) REVERT: C 84 ASN cc_start: 0.8272 (t0) cc_final: 0.7804 (t0) REVERT: C 91 VAL cc_start: 0.8704 (t) cc_final: 0.8430 (p) REVERT: C 121 LEU cc_start: 0.7884 (tp) cc_final: 0.7679 (tp) REVERT: C 128 GLN cc_start: 0.7670 (mm-40) cc_final: 0.6734 (mm-40) REVERT: C 143 LEU cc_start: 0.8830 (mt) cc_final: 0.8580 (mt) REVERT: C 150 HIS cc_start: 0.8771 (m-70) cc_final: 0.8538 (m90) REVERT: C 159 CYS cc_start: 0.7969 (t) cc_final: 0.7390 (t) REVERT: C 170 LEU cc_start: 0.8351 (mt) cc_final: 0.8101 (tp) REVERT: C 172 TRP cc_start: 0.8398 (t60) cc_final: 0.7347 (t60) REVERT: b 43 LYS cc_start: 0.8379 (mttt) cc_final: 0.7952 (tttm) REVERT: b 49 GLN cc_start: 0.8647 (mt0) cc_final: 0.8381 (pt0) REVERT: b 50 MET cc_start: 0.8584 (mtm) cc_final: 0.8236 (mpp) REVERT: b 51 LEU cc_start: 0.8612 (mt) cc_final: 0.8278 (mt) REVERT: b 52 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7712 (mm-30) REVERT: b 54 ASN cc_start: 0.7883 (p0) cc_final: 0.7409 (t0) REVERT: b 55 LYS cc_start: 0.8213 (ttpt) cc_final: 0.7971 (mtmt) REVERT: b 59 LYS cc_start: 0.8483 (mttm) cc_final: 0.8216 (mttp) REVERT: b 63 MET cc_start: 0.8454 (mmm) cc_final: 0.8045 (mmm) REVERT: b 72 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8451 (mtmt) REVERT: b 97 LEU cc_start: 0.8942 (mt) cc_final: 0.8424 (mm) REVERT: b 101 TYR cc_start: 0.8576 (t80) cc_final: 0.8361 (t80) REVERT: b 119 THR cc_start: 0.8445 (t) cc_final: 0.8070 (m) REVERT: b 121 GLN cc_start: 0.8155 (tt0) cc_final: 0.7882 (mt0) REVERT: b 131 ILE cc_start: 0.8647 (mt) cc_final: 0.8429 (mm) REVERT: b 132 ARG cc_start: 0.8532 (mtt180) cc_final: 0.8092 (ttm170) REVERT: b 141 SER cc_start: 0.8552 (m) cc_final: 0.8149 (t) REVERT: b 165 TYR cc_start: 0.8641 (t80) cc_final: 0.8400 (t80) REVERT: b 169 ASN cc_start: 0.8742 (m-40) cc_final: 0.8347 (t0) REVERT: b 175 GLN cc_start: 0.8372 (tm-30) cc_final: 0.8158 (tm-30) REVERT: b 181 ASP cc_start: 0.7968 (t0) cc_final: 0.7439 (t0) REVERT: b 183 GLU cc_start: 0.8809 (mm-30) cc_final: 0.7736 (tm-30) REVERT: b 185 LYS cc_start: 0.7920 (tttt) cc_final: 0.7614 (ttpp) REVERT: b 190 GLU cc_start: 0.8019 (tt0) cc_final: 0.7112 (tt0) REVERT: b 191 VAL cc_start: 0.8948 (t) cc_final: 0.8220 (t) REVERT: b 193 GLU cc_start: 0.8400 (tt0) cc_final: 0.8182 (tt0) REVERT: b 194 LYS cc_start: 0.9013 (mttt) cc_final: 0.8439 (mttt) REVERT: b 195 LEU cc_start: 0.8780 (mt) cc_final: 0.8468 (mt) REVERT: b 196 LEU cc_start: 0.8508 (mt) cc_final: 0.8054 (tp) REVERT: b 215 CYS cc_start: 0.7862 (t) cc_final: 0.7008 (t) REVERT: b 226 TYR cc_start: 0.7891 (t80) cc_final: 0.7583 (t80) REVERT: b 237 GLU cc_start: 0.7553 (tt0) cc_final: 0.7332 (tt0) REVERT: b 241 GLN cc_start: 0.8367 (mt0) cc_final: 0.7574 (mt0) REVERT: b 244 ILE cc_start: 0.9182 (mt) cc_final: 0.8751 (tp) REVERT: b 246 HIS cc_start: 0.8403 (m-70) cc_final: 0.7945 (m-70) REVERT: b 247 MET cc_start: 0.7488 (tmm) cc_final: 0.7098 (tmm) REVERT: b 298 ARG cc_start: 0.8425 (mmm160) cc_final: 0.7682 (mpt180) REVERT: b 300 LEU cc_start: 0.8681 (tp) cc_final: 0.8459 (tp) REVERT: b 303 ASN cc_start: 0.8493 (m-40) cc_final: 0.7793 (t0) REVERT: b 305 LYS cc_start: 0.8984 (tttt) cc_final: 0.8735 (ttpp) REVERT: b 307 LEU cc_start: 0.8962 (mt) cc_final: 0.8726 (mm) REVERT: b 308 LEU cc_start: 0.8483 (mt) cc_final: 0.8205 (mm) REVERT: b 311 ARG cc_start: 0.8250 (ptt180) cc_final: 0.7736 (ptt-90) REVERT: b 317 MET cc_start: 0.8587 (tpp) cc_final: 0.8202 (tpt) REVERT: b 321 GLN cc_start: 0.7724 (tt0) cc_final: 0.7485 (tt0) REVERT: b 326 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7912 (mm) REVERT: b 355 GLN cc_start: 0.8464 (mt0) cc_final: 0.8242 (mt0) REVERT: b 359 THR cc_start: 0.7643 (m) cc_final: 0.7411 (p) REVERT: b 411 THR cc_start: 0.8470 (m) cc_final: 0.8097 (p) REVERT: b 417 ASP cc_start: 0.7850 (t0) cc_final: 0.7535 (m-30) REVERT: b 640 PRO cc_start: 0.8598 (Cg_exo) cc_final: 0.8240 (Cg_endo) REVERT: m 1 MET cc_start: 0.6831 (mtt) cc_final: 0.6378 (mtt) REVERT: m 29 CYS cc_start: 0.8387 (m) cc_final: 0.7948 (t) REVERT: m 33 PHE cc_start: 0.8540 (m-80) cc_final: 0.8196 (m-80) REVERT: m 36 GLN cc_start: 0.8554 (tp40) cc_final: 0.8333 (tp40) REVERT: m 43 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7382 (mt-10) REVERT: m 53 HIS cc_start: 0.8043 (m-70) cc_final: 0.7839 (m-70) REVERT: m 55 TYR cc_start: 0.8044 (m-80) cc_final: 0.7828 (m-80) REVERT: m 64 LEU cc_start: 0.8638 (tp) cc_final: 0.8411 (tp) REVERT: m 77 LEU cc_start: 0.8732 (mt) cc_final: 0.8415 (mp) REVERT: m 78 PHE cc_start: 0.9036 (t80) cc_final: 0.8817 (t80) REVERT: m 81 GLU cc_start: 0.7411 (tp30) cc_final: 0.6606 (tp30) REVERT: m 108 ILE cc_start: 0.8758 (mt) cc_final: 0.8530 (mm) REVERT: m 115 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7686 (tp30) REVERT: m 116 MET cc_start: 0.7588 (mtm) cc_final: 0.6964 (mtm) REVERT: m 119 ASN cc_start: 0.8344 (t0) cc_final: 0.7968 (t0) REVERT: m 126 GLU cc_start: 0.8075 (tp30) cc_final: 0.7758 (tp30) REVERT: m 134 ILE cc_start: 0.8057 (mt) cc_final: 0.7473 (mt) REVERT: m 157 LEU cc_start: 0.8414 (mt) cc_final: 0.8032 (pp) REVERT: m 158 PRO cc_start: 0.8357 (Cg_exo) cc_final: 0.7542 (Cg_endo) REVERT: m 173 LYS cc_start: 0.7504 (tttt) cc_final: 0.7230 (tttt) REVERT: m 181 PHE cc_start: 0.8079 (m-80) cc_final: 0.7751 (m-80) REVERT: m 182 ASP cc_start: 0.6706 (m-30) cc_final: 0.6303 (m-30) REVERT: m 203 GLN cc_start: 0.7347 (mm-40) cc_final: 0.7091 (mm-40) REVERT: m 209 CYS cc_start: 0.7581 (t) cc_final: 0.6507 (m) REVERT: m 234 HIS cc_start: 0.7295 (t-90) cc_final: 0.6932 (t-90) REVERT: m 240 LYS cc_start: 0.8505 (mttt) cc_final: 0.8059 (mtpp) REVERT: m 257 PHE cc_start: 0.8217 (p90) cc_final: 0.7885 (p90) REVERT: m 258 ARG cc_start: 0.8235 (mtm180) cc_final: 0.7960 (mtm-85) REVERT: m 259 LEU cc_start: 0.8606 (tp) cc_final: 0.8293 (tp) REVERT: m 272 ILE cc_start: 0.6702 (mm) cc_final: 0.5993 (mm) REVERT: m 274 VAL cc_start: 0.7682 (t) cc_final: 0.7462 (p) REVERT: m 298 LYS cc_start: 0.8417 (tttt) cc_final: 0.8147 (tttt) REVERT: m 300 ASN cc_start: 0.8585 (p0) cc_final: 0.8215 (p0) REVERT: m 373 LEU cc_start: 0.6589 (tp) cc_final: 0.6261 (tt) REVERT: m 377 PHE cc_start: 0.8233 (p90) cc_final: 0.7649 (p90) REVERT: m 414 PHE cc_start: 0.7743 (t80) cc_final: 0.7007 (t80) REVERT: c 18 MET cc_start: 0.6253 (mmt) cc_final: 0.6033 (mmt) REVERT: c 21 LEU cc_start: 0.8527 (tp) cc_final: 0.8263 (tp) REVERT: c 39 LEU cc_start: 0.8462 (mt) cc_final: 0.8247 (mt) REVERT: c 45 THR cc_start: 0.8798 (p) cc_final: 0.8510 (t) REVERT: c 64 THR cc_start: 0.7127 (m) cc_final: 0.6578 (t) REVERT: c 82 PHE cc_start: 0.8259 (m-10) cc_final: 0.8036 (m-80) REVERT: c 84 ASN cc_start: 0.8359 (t0) cc_final: 0.6710 (t0) REVERT: c 91 VAL cc_start: 0.8581 (t) cc_final: 0.8316 (t) REVERT: c 110 MET cc_start: 0.8495 (mmm) cc_final: 0.7974 (mmm) REVERT: c 118 ASP cc_start: 0.8165 (m-30) cc_final: 0.7958 (t0) REVERT: c 168 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8132 (mt-10) outliers start: 8 outliers final: 4 residues processed: 834 average time/residue: 0.1391 time to fit residues: 165.8706 Evaluate side-chains 791 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 785 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.4980 chunk 149 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 169 ASN B 309 GLN B 321 GLN ** B 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 161 GLN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 309 GLN b 321 GLN ** b 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 54 HIS m 161 GLN ** m 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 380 GLN ** c 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.139304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.115226 restraints weight = 31033.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.119574 restraints weight = 16515.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.122548 restraints weight = 10169.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.124294 restraints weight = 6945.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.125948 restraints weight = 5229.919| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16108 Z= 0.185 Angle : 0.671 7.694 21822 Z= 0.360 Chirality : 0.047 0.178 2524 Planarity : 0.005 0.055 2752 Dihedral : 11.397 178.212 2154 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.17 % Allowed : 1.42 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.20), residues: 1954 helix: 0.67 (0.18), residues: 818 sheet: 0.03 (0.27), residues: 360 loop : 1.36 (0.25), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 79 TYR 0.021 0.003 TYR C 58 PHE 0.015 0.002 PHE M 66 TRP 0.020 0.002 TRP m 242 HIS 0.003 0.001 HIS M 84 Details of bonding type rmsd covalent geometry : bond 0.00364 (16108) covalent geometry : angle 0.67143 (21822) hydrogen bonds : bond 0.05442 ( 815) hydrogen bonds : angle 5.89574 ( 2361) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 810 time to evaluate : 0.647 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: B 43 LYS cc_start: 0.8268 (mttt) cc_final: 0.7547 (mmmt) REVERT: B 45 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7411 (mm-30) REVERT: B 48 LYS cc_start: 0.8928 (mtmt) cc_final: 0.8520 (mtmm) REVERT: B 50 MET cc_start: 0.8647 (mtm) cc_final: 0.8247 (mtm) REVERT: B 63 MET cc_start: 0.8464 (mmm) cc_final: 0.7733 (mmm) REVERT: B 64 LYS cc_start: 0.8947 (mttt) cc_final: 0.8512 (mtpp) REVERT: B 72 LYS cc_start: 0.8789 (mmtt) cc_final: 0.8435 (mtmt) REVERT: B 74 LYS cc_start: 0.8637 (mmtt) cc_final: 0.8360 (mmtt) REVERT: B 79 LEU cc_start: 0.8498 (mt) cc_final: 0.8274 (mt) REVERT: B 80 PHE cc_start: 0.8442 (t80) cc_final: 0.7807 (t80) REVERT: B 83 VAL cc_start: 0.8390 (t) cc_final: 0.8012 (t) REVERT: B 85 LYS cc_start: 0.8663 (mttt) cc_final: 0.8381 (mttt) REVERT: B 90 LYS cc_start: 0.8267 (mttt) cc_final: 0.7878 (mttt) REVERT: B 94 ILE cc_start: 0.8315 (mt) cc_final: 0.8004 (mm) REVERT: B 101 TYR cc_start: 0.8512 (t80) cc_final: 0.8119 (t80) REVERT: B 112 LEU cc_start: 0.8297 (mt) cc_final: 0.7619 (mp) REVERT: B 125 LYS cc_start: 0.8745 (mttt) cc_final: 0.8345 (mtpp) REVERT: B 132 ARG cc_start: 0.8421 (mtt180) cc_final: 0.8074 (ttm170) REVERT: B 139 LEU cc_start: 0.8396 (tp) cc_final: 0.8184 (tt) REVERT: B 141 SER cc_start: 0.8402 (m) cc_final: 0.8165 (m) REVERT: B 142 ILE cc_start: 0.8959 (mm) cc_final: 0.8617 (mp) REVERT: B 151 MET cc_start: 0.7950 (mtp) cc_final: 0.7653 (mtp) REVERT: B 166 VAL cc_start: 0.8631 (t) cc_final: 0.8384 (p) REVERT: B 190 GLU cc_start: 0.8221 (tt0) cc_final: 0.8009 (tt0) REVERT: B 191 VAL cc_start: 0.9045 (t) cc_final: 0.8798 (p) REVERT: B 193 GLU cc_start: 0.8394 (tt0) cc_final: 0.8148 (tt0) REVERT: B 196 LEU cc_start: 0.8550 (mt) cc_final: 0.8328 (tp) REVERT: B 202 LEU cc_start: 0.7693 (mm) cc_final: 0.7332 (tp) REVERT: B 207 VAL cc_start: 0.8949 (t) cc_final: 0.8640 (p) REVERT: B 215 CYS cc_start: 0.8230 (t) cc_final: 0.7986 (t) REVERT: B 246 HIS cc_start: 0.8335 (m-70) cc_final: 0.8109 (m-70) REVERT: B 247 MET cc_start: 0.7488 (tmm) cc_final: 0.6951 (tmm) REVERT: B 298 ARG cc_start: 0.8528 (mmm160) cc_final: 0.7764 (mpt180) REVERT: B 305 LYS cc_start: 0.8717 (tttt) cc_final: 0.8225 (ttpp) REVERT: B 308 LEU cc_start: 0.8532 (mt) cc_final: 0.8273 (mm) REVERT: B 311 ARG cc_start: 0.8384 (ptt180) cc_final: 0.7746 (ptt-90) REVERT: B 321 GLN cc_start: 0.8003 (tt0) cc_final: 0.7729 (tt0) REVERT: B 322 LEU cc_start: 0.8402 (tt) cc_final: 0.8182 (tt) REVERT: B 324 TRP cc_start: 0.8779 (t-100) cc_final: 0.8505 (t-100) REVERT: B 326 ILE cc_start: 0.8029 (mm) cc_final: 0.7729 (mm) REVERT: B 341 ARG cc_start: 0.8736 (ptt90) cc_final: 0.8363 (ptm-80) REVERT: B 348 GLU cc_start: 0.8116 (mp0) cc_final: 0.7911 (mp0) REVERT: B 349 VAL cc_start: 0.8308 (t) cc_final: 0.8083 (t) REVERT: B 387 THR cc_start: 0.8466 (m) cc_final: 0.8195 (m) REVERT: B 388 LEU cc_start: 0.8640 (mt) cc_final: 0.8419 (mm) REVERT: B 391 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6950 (mt-10) REVERT: B 417 ASP cc_start: 0.8040 (t0) cc_final: 0.7813 (t0) REVERT: M 1 MET cc_start: 0.6739 (mtt) cc_final: 0.6410 (mtt) REVERT: M 17 GLU cc_start: 0.7737 (pt0) cc_final: 0.7439 (pt0) REVERT: M 21 LYS cc_start: 0.8088 (mttt) cc_final: 0.7232 (mtpp) REVERT: M 43 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7450 (mt-10) REVERT: M 56 LEU cc_start: 0.8428 (mp) cc_final: 0.8225 (mm) REVERT: M 62 ASP cc_start: 0.8157 (m-30) cc_final: 0.7845 (m-30) REVERT: M 67 VAL cc_start: 0.8184 (t) cc_final: 0.7868 (m) REVERT: M 71 GLN cc_start: 0.8324 (tp40) cc_final: 0.7835 (tp40) REVERT: M 74 VAL cc_start: 0.8901 (t) cc_final: 0.8480 (p) REVERT: M 78 PHE cc_start: 0.8857 (t80) cc_final: 0.8532 (t80) REVERT: M 89 THR cc_start: 0.8914 (m) cc_final: 0.8427 (p) REVERT: M 90 PHE cc_start: 0.8608 (m-10) cc_final: 0.8379 (m-10) REVERT: M 108 ILE cc_start: 0.8830 (mt) cc_final: 0.8610 (mt) REVERT: M 116 MET cc_start: 0.7785 (mtm) cc_final: 0.7311 (mtm) REVERT: M 119 ASN cc_start: 0.8392 (t0) cc_final: 0.7833 (t0) REVERT: M 121 PHE cc_start: 0.7726 (t80) cc_final: 0.7190 (t80) REVERT: M 126 GLU cc_start: 0.8091 (tp30) cc_final: 0.7437 (tp30) REVERT: M 128 ASN cc_start: 0.8601 (m-40) cc_final: 0.7876 (m110) REVERT: M 131 LYS cc_start: 0.8561 (mttp) cc_final: 0.8017 (mttp) REVERT: M 134 ILE cc_start: 0.8381 (mt) cc_final: 0.7901 (mt) REVERT: M 135 LYS cc_start: 0.8856 (mmtt) cc_final: 0.8325 (mmtt) REVERT: M 153 VAL cc_start: 0.7893 (t) cc_final: 0.7527 (m) REVERT: M 157 LEU cc_start: 0.8364 (mt) cc_final: 0.8075 (pp) REVERT: M 159 THR cc_start: 0.8059 (m) cc_final: 0.7751 (t) REVERT: M 173 LYS cc_start: 0.7770 (tttt) cc_final: 0.7453 (tttt) REVERT: M 174 TYR cc_start: 0.7042 (m-80) cc_final: 0.6831 (m-80) REVERT: M 183 VAL cc_start: 0.8321 (t) cc_final: 0.8009 (p) REVERT: M 209 CYS cc_start: 0.7552 (t) cc_final: 0.6961 (t) REVERT: M 210 ILE cc_start: 0.8583 (mm) cc_final: 0.8350 (mm) REVERT: M 227 LEU cc_start: 0.9006 (mt) cc_final: 0.8639 (mp) REVERT: M 240 LYS cc_start: 0.8497 (mttt) cc_final: 0.8146 (mttt) REVERT: M 242 TRP cc_start: 0.7134 (t-100) cc_final: 0.6898 (t-100) REVERT: M 257 PHE cc_start: 0.8340 (p90) cc_final: 0.8007 (p90) REVERT: M 258 ARG cc_start: 0.8245 (mtm180) cc_final: 0.7914 (mtm-85) REVERT: M 262 TYR cc_start: 0.8371 (p90) cc_final: 0.7962 (p90) REVERT: M 298 LYS cc_start: 0.8889 (tttt) cc_final: 0.8484 (tttt) REVERT: M 300 ASN cc_start: 0.8894 (p0) cc_final: 0.8634 (p0) REVERT: M 345 LYS cc_start: 0.7197 (ptmm) cc_final: 0.6321 (mtpp) REVERT: M 377 PHE cc_start: 0.7895 (p90) cc_final: 0.7447 (p90) REVERT: M 393 ASP cc_start: 0.8019 (t0) cc_final: 0.7658 (t0) REVERT: M 402 PHE cc_start: 0.7567 (m-80) cc_final: 0.7109 (m-80) REVERT: M 407 TYR cc_start: 0.8542 (m-80) cc_final: 0.8127 (m-80) REVERT: M 414 PHE cc_start: 0.7763 (t80) cc_final: 0.7185 (t80) REVERT: C 21 LEU cc_start: 0.8378 (tp) cc_final: 0.8118 (tp) REVERT: C 51 PHE cc_start: 0.8122 (p90) cc_final: 0.7838 (p90) REVERT: C 58 TYR cc_start: 0.7928 (t80) cc_final: 0.7412 (t80) REVERT: C 64 THR cc_start: 0.6783 (m) cc_final: 0.6553 (t) REVERT: C 78 TRP cc_start: 0.8140 (m-10) cc_final: 0.7659 (m-10) REVERT: C 81 TYR cc_start: 0.7281 (m-80) cc_final: 0.6789 (m-80) REVERT: C 82 PHE cc_start: 0.7843 (m-10) cc_final: 0.7641 (m-80) REVERT: C 84 ASN cc_start: 0.8363 (t0) cc_final: 0.7719 (t0) REVERT: C 86 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7484 (mt0) REVERT: C 110 MET cc_start: 0.8327 (mmm) cc_final: 0.7662 (mmm) REVERT: C 116 LEU cc_start: 0.7848 (mt) cc_final: 0.7596 (mt) REVERT: C 128 GLN cc_start: 0.7249 (mm-40) cc_final: 0.6541 (mm-40) REVERT: C 143 LEU cc_start: 0.8843 (mt) cc_final: 0.8619 (mt) REVERT: C 145 LEU cc_start: 0.8280 (mt) cc_final: 0.8036 (mt) REVERT: C 150 HIS cc_start: 0.8567 (m-70) cc_final: 0.8351 (m90) REVERT: C 153 TRP cc_start: 0.8523 (p-90) cc_final: 0.7987 (p-90) REVERT: C 159 CYS cc_start: 0.8304 (t) cc_final: 0.7891 (t) REVERT: C 167 TYR cc_start: 0.7844 (m-10) cc_final: 0.7136 (m-80) REVERT: C 168 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7884 (mt-10) REVERT: C 171 ASP cc_start: 0.8354 (m-30) cc_final: 0.8023 (m-30) REVERT: C 172 TRP cc_start: 0.8231 (t60) cc_final: 0.7383 (t60) REVERT: C 176 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7417 (mm-40) REVERT: b 43 LYS cc_start: 0.8163 (mttt) cc_final: 0.7778 (tttp) REVERT: b 50 MET cc_start: 0.8614 (mtm) cc_final: 0.8334 (mpp) REVERT: b 54 ASN cc_start: 0.7616 (p0) cc_final: 0.7042 (t0) REVERT: b 55 LYS cc_start: 0.8383 (ttpt) cc_final: 0.7810 (mtpt) REVERT: b 59 LYS cc_start: 0.8681 (mttm) cc_final: 0.8398 (mttt) REVERT: b 63 MET cc_start: 0.8467 (mmm) cc_final: 0.7661 (mmm) REVERT: b 72 LYS cc_start: 0.8776 (mmtt) cc_final: 0.8360 (mtmt) REVERT: b 79 LEU cc_start: 0.8533 (mt) cc_final: 0.8208 (mt) REVERT: b 83 VAL cc_start: 0.8284 (t) cc_final: 0.7981 (t) REVERT: b 85 LYS cc_start: 0.8653 (mttt) cc_final: 0.8432 (mttt) REVERT: b 90 LYS cc_start: 0.8168 (mttm) cc_final: 0.7915 (ttmm) REVERT: b 97 LEU cc_start: 0.8805 (mt) cc_final: 0.8248 (mt) REVERT: b 101 TYR cc_start: 0.8551 (t80) cc_final: 0.8325 (t80) REVERT: b 112 LEU cc_start: 0.8063 (mp) cc_final: 0.7682 (mp) REVERT: b 131 ILE cc_start: 0.8564 (mt) cc_final: 0.8362 (mm) REVERT: b 132 ARG cc_start: 0.8485 (mtt180) cc_final: 0.8130 (ttm170) REVERT: b 139 LEU cc_start: 0.8331 (tp) cc_final: 0.8086 (tt) REVERT: b 141 SER cc_start: 0.8458 (m) cc_final: 0.7912 (t) REVERT: b 142 ILE cc_start: 0.8996 (mm) cc_final: 0.8603 (mp) REVERT: b 147 ILE cc_start: 0.8570 (pt) cc_final: 0.8365 (pt) REVERT: b 151 MET cc_start: 0.7737 (mtp) cc_final: 0.7340 (mtp) REVERT: b 166 VAL cc_start: 0.8677 (t) cc_final: 0.8445 (p) REVERT: b 177 LEU cc_start: 0.8569 (tp) cc_final: 0.8368 (tp) REVERT: b 181 ASP cc_start: 0.8100 (t0) cc_final: 0.7632 (t0) REVERT: b 185 LYS cc_start: 0.7859 (tttt) cc_final: 0.7406 (ttpp) REVERT: b 191 VAL cc_start: 0.8997 (t) cc_final: 0.8763 (p) REVERT: b 195 LEU cc_start: 0.9010 (mt) cc_final: 0.8690 (mt) REVERT: b 196 LEU cc_start: 0.8631 (mt) cc_final: 0.8239 (tp) REVERT: b 202 LEU cc_start: 0.7831 (mm) cc_final: 0.7379 (tt) REVERT: b 207 VAL cc_start: 0.8943 (t) cc_final: 0.8529 (p) REVERT: b 212 GLU cc_start: 0.8328 (tp30) cc_final: 0.8084 (tp30) REVERT: b 215 CYS cc_start: 0.8292 (t) cc_final: 0.8091 (t) REVERT: b 228 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8023 (ttpt) REVERT: b 244 ILE cc_start: 0.9122 (mt) cc_final: 0.8728 (tp) REVERT: b 247 MET cc_start: 0.7568 (tmm) cc_final: 0.6586 (tmm) REVERT: b 298 ARG cc_start: 0.8666 (mmm160) cc_final: 0.7457 (mpt180) REVERT: b 305 LYS cc_start: 0.8694 (tttt) cc_final: 0.8459 (tttm) REVERT: b 307 LEU cc_start: 0.8917 (mt) cc_final: 0.8671 (mm) REVERT: b 308 LEU cc_start: 0.8637 (mt) cc_final: 0.8312 (mm) REVERT: b 311 ARG cc_start: 0.8405 (ptt180) cc_final: 0.7793 (ptt-90) REVERT: b 317 MET cc_start: 0.8796 (tpp) cc_final: 0.8523 (tpt) REVERT: b 321 GLN cc_start: 0.7981 (tt0) cc_final: 0.7646 (tt0) REVERT: b 322 LEU cc_start: 0.8542 (tt) cc_final: 0.8257 (tt) REVERT: b 326 ILE cc_start: 0.8128 (mm) cc_final: 0.7833 (mm) REVERT: b 341 ARG cc_start: 0.8729 (ptt90) cc_final: 0.8239 (ptm-80) REVERT: b 348 GLU cc_start: 0.8299 (mp0) cc_final: 0.8052 (mp0) REVERT: b 349 VAL cc_start: 0.8336 (t) cc_final: 0.8121 (t) REVERT: b 352 ILE cc_start: 0.8596 (mm) cc_final: 0.8372 (mm) REVERT: b 417 ASP cc_start: 0.7746 (t0) cc_final: 0.7209 (t0) REVERT: b 629 LYS cc_start: 0.7808 (ttmt) cc_final: 0.7509 (ttmm) REVERT: b 645 ASP cc_start: 0.7794 (t0) cc_final: 0.7083 (p0) REVERT: m 1 MET cc_start: 0.6895 (mtt) cc_final: 0.6358 (mtt) REVERT: m 14 ILE cc_start: 0.8009 (mt) cc_final: 0.7704 (mt) REVERT: m 17 GLU cc_start: 0.7697 (pt0) cc_final: 0.7390 (pt0) REVERT: m 24 VAL cc_start: 0.8608 (t) cc_final: 0.8258 (p) REVERT: m 29 CYS cc_start: 0.8459 (m) cc_final: 0.7927 (t) REVERT: m 33 PHE cc_start: 0.8605 (m-80) cc_final: 0.8159 (m-80) REVERT: m 36 GLN cc_start: 0.8488 (tp40) cc_final: 0.8065 (tp40) REVERT: m 43 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7453 (mt-10) REVERT: m 53 HIS cc_start: 0.8226 (m-70) cc_final: 0.7828 (m170) REVERT: m 60 TYR cc_start: 0.7967 (t80) cc_final: 0.7705 (t80) REVERT: m 64 LEU cc_start: 0.8325 (tp) cc_final: 0.8114 (tp) REVERT: m 71 GLN cc_start: 0.8354 (tp40) cc_final: 0.7686 (tp40) REVERT: m 78 PHE cc_start: 0.8828 (t80) cc_final: 0.8530 (t80) REVERT: m 81 GLU cc_start: 0.7606 (tp30) cc_final: 0.7293 (tp30) REVERT: m 88 ASP cc_start: 0.8589 (m-30) cc_final: 0.8311 (m-30) REVERT: m 92 ASP cc_start: 0.7608 (t70) cc_final: 0.7261 (t70) REVERT: m 103 LYS cc_start: 0.7456 (mtmm) cc_final: 0.7158 (mtmm) REVERT: m 108 ILE cc_start: 0.8800 (mt) cc_final: 0.8431 (mm) REVERT: m 116 MET cc_start: 0.7570 (mtm) cc_final: 0.7016 (mtm) REVERT: m 119 ASN cc_start: 0.8379 (t0) cc_final: 0.8176 (t0) REVERT: m 125 THR cc_start: 0.8545 (m) cc_final: 0.8222 (t) REVERT: m 126 GLU cc_start: 0.8150 (tp30) cc_final: 0.7588 (tp30) REVERT: m 128 ASN cc_start: 0.8578 (m-40) cc_final: 0.7610 (m-40) REVERT: m 131 LYS cc_start: 0.8554 (mttp) cc_final: 0.8155 (mttt) REVERT: m 134 ILE cc_start: 0.8176 (mt) cc_final: 0.7492 (tp) REVERT: m 140 LEU cc_start: 0.8512 (mt) cc_final: 0.8262 (tt) REVERT: m 141 ARG cc_start: 0.8226 (mmt90) cc_final: 0.7791 (mmt90) REVERT: m 173 LYS cc_start: 0.7885 (tttt) cc_final: 0.7660 (tttt) REVERT: m 183 VAL cc_start: 0.8311 (t) cc_final: 0.8084 (p) REVERT: m 209 CYS cc_start: 0.7390 (t) cc_final: 0.6323 (m) REVERT: m 220 LEU cc_start: 0.8273 (mm) cc_final: 0.7891 (mm) REVERT: m 234 HIS cc_start: 0.7812 (t-90) cc_final: 0.7334 (t-90) REVERT: m 240 LYS cc_start: 0.8649 (mttt) cc_final: 0.7997 (mmmm) REVERT: m 257 PHE cc_start: 0.8357 (p90) cc_final: 0.7998 (p90) REVERT: m 258 ARG cc_start: 0.8255 (mtm180) cc_final: 0.7985 (mtm-85) REVERT: m 272 ILE cc_start: 0.7538 (mm) cc_final: 0.6847 (mm) REVERT: m 274 VAL cc_start: 0.7938 (t) cc_final: 0.7662 (p) REVERT: m 298 LYS cc_start: 0.8961 (tttt) cc_final: 0.8572 (tttt) REVERT: m 300 ASN cc_start: 0.9022 (p0) cc_final: 0.8803 (p0) REVERT: m 342 ASP cc_start: 0.8124 (t0) cc_final: 0.7879 (t0) REVERT: m 377 PHE cc_start: 0.7760 (p90) cc_final: 0.7384 (p90) REVERT: m 402 PHE cc_start: 0.7488 (m-80) cc_final: 0.6877 (m-80) REVERT: m 414 PHE cc_start: 0.7937 (t80) cc_final: 0.7253 (t80) REVERT: c 18 MET cc_start: 0.6132 (mmt) cc_final: 0.5728 (mmt) REVERT: c 19 ARG cc_start: 0.7109 (ttm170) cc_final: 0.6853 (ttm170) REVERT: c 21 LEU cc_start: 0.8434 (tp) cc_final: 0.8199 (tp) REVERT: c 45 THR cc_start: 0.8998 (p) cc_final: 0.8611 (t) REVERT: c 53 VAL cc_start: 0.8498 (p) cc_final: 0.8286 (t) REVERT: c 58 TYR cc_start: 0.7963 (t80) cc_final: 0.7258 (t80) REVERT: c 64 THR cc_start: 0.6847 (m) cc_final: 0.6399 (t) REVERT: c 84 ASN cc_start: 0.8003 (t0) cc_final: 0.7128 (t0) REVERT: c 86 GLN cc_start: 0.7758 (mm-40) cc_final: 0.6946 (mt0) REVERT: c 110 MET cc_start: 0.8273 (mmm) cc_final: 0.7777 (mmm) REVERT: c 128 GLN cc_start: 0.7393 (mm-40) cc_final: 0.7136 (mm-40) REVERT: c 151 ARG cc_start: 0.8308 (ttm-80) cc_final: 0.7986 (ttm-80) REVERT: c 159 CYS cc_start: 0.8451 (t) cc_final: 0.8086 (t) REVERT: c 167 TYR cc_start: 0.7898 (m-10) cc_final: 0.7245 (m-80) REVERT: c 168 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8007 (mt-10) REVERT: c 171 ASP cc_start: 0.8479 (m-30) cc_final: 0.8164 (m-30) outliers start: 3 outliers final: 2 residues processed: 812 average time/residue: 0.1432 time to fit residues: 166.2031 Evaluate side-chains 767 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 765 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 95 optimal weight: 3.9990 chunk 176 optimal weight: 0.7980 chunk 122 optimal weight: 0.0070 chunk 121 optimal weight: 0.4980 chunk 140 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 158 optimal weight: 0.0070 chunk 25 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 GLN ** M 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 355 GLN m 19 HIS m 26 GLN m 54 HIS c 95 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.142169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.117268 restraints weight = 31211.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.121648 restraints weight = 16693.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.124702 restraints weight = 10433.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.126803 restraints weight = 7112.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.128399 restraints weight = 5245.126| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16108 Z= 0.135 Angle : 0.586 7.186 21822 Z= 0.310 Chirality : 0.045 0.164 2524 Planarity : 0.004 0.039 2752 Dihedral : 10.818 171.265 2154 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.06 % Allowed : 1.76 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.20), residues: 1954 helix: 1.02 (0.18), residues: 810 sheet: 0.04 (0.27), residues: 370 loop : 1.44 (0.25), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 79 TYR 0.027 0.002 TYR M 110 PHE 0.028 0.002 PHE c 82 TRP 0.027 0.002 TRP C 66 HIS 0.005 0.001 HIS b 624 Details of bonding type rmsd covalent geometry : bond 0.00270 (16108) covalent geometry : angle 0.58626 (21822) hydrogen bonds : bond 0.04695 ( 815) hydrogen bonds : angle 5.42915 ( 2361) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 807 time to evaluate : 0.631 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: B 43 LYS cc_start: 0.8253 (mttt) cc_final: 0.7574 (mmmt) REVERT: B 50 MET cc_start: 0.8548 (mtm) cc_final: 0.8098 (mtm) REVERT: B 51 LEU cc_start: 0.8700 (mt) cc_final: 0.8377 (mt) REVERT: B 52 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7430 (mm-30) REVERT: B 59 LYS cc_start: 0.8797 (mttm) cc_final: 0.8596 (mttt) REVERT: B 63 MET cc_start: 0.8494 (mmm) cc_final: 0.7674 (mmm) REVERT: B 72 LYS cc_start: 0.8794 (mmtt) cc_final: 0.8394 (mtpt) REVERT: B 74 LYS cc_start: 0.8715 (mmtt) cc_final: 0.8404 (mmtt) REVERT: B 79 LEU cc_start: 0.8619 (mt) cc_final: 0.8402 (mt) REVERT: B 80 PHE cc_start: 0.8445 (t80) cc_final: 0.7494 (t80) REVERT: B 83 VAL cc_start: 0.8449 (t) cc_final: 0.8211 (t) REVERT: B 84 VAL cc_start: 0.8640 (p) cc_final: 0.8318 (m) REVERT: B 85 LYS cc_start: 0.8689 (mttt) cc_final: 0.8096 (mttt) REVERT: B 90 LYS cc_start: 0.8227 (mttt) cc_final: 0.7974 (mttt) REVERT: B 94 ILE cc_start: 0.8223 (mt) cc_final: 0.8000 (mm) REVERT: B 101 TYR cc_start: 0.8488 (t80) cc_final: 0.8222 (t80) REVERT: B 104 ARG cc_start: 0.8768 (tpt90) cc_final: 0.8510 (tpt90) REVERT: B 112 LEU cc_start: 0.8133 (mt) cc_final: 0.7558 (mp) REVERT: B 121 GLN cc_start: 0.8398 (tt0) cc_final: 0.8022 (mt0) REVERT: B 125 LYS cc_start: 0.8825 (mttt) cc_final: 0.8408 (mtpp) REVERT: B 132 ARG cc_start: 0.8424 (mtt180) cc_final: 0.7887 (ttm110) REVERT: B 141 SER cc_start: 0.8421 (m) cc_final: 0.8157 (m) REVERT: B 142 ILE cc_start: 0.8946 (mm) cc_final: 0.8641 (mp) REVERT: B 151 MET cc_start: 0.7804 (mtp) cc_final: 0.7451 (mtp) REVERT: B 152 MET cc_start: 0.8158 (tpt) cc_final: 0.7866 (tpt) REVERT: B 155 ILE cc_start: 0.9213 (mm) cc_final: 0.9009 (mm) REVERT: B 166 VAL cc_start: 0.8673 (t) cc_final: 0.8465 (p) REVERT: B 167 ARG cc_start: 0.8401 (mtp180) cc_final: 0.7580 (mtm-85) REVERT: B 169 ASN cc_start: 0.8724 (m-40) cc_final: 0.8493 (m-40) REVERT: B 175 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8096 (tm-30) REVERT: B 187 MET cc_start: 0.8295 (mtm) cc_final: 0.8027 (ptp) REVERT: B 191 VAL cc_start: 0.8997 (t) cc_final: 0.8777 (p) REVERT: B 193 GLU cc_start: 0.8364 (tt0) cc_final: 0.8119 (tt0) REVERT: B 195 LEU cc_start: 0.8989 (mm) cc_final: 0.8543 (mt) REVERT: B 196 LEU cc_start: 0.8620 (mt) cc_final: 0.8344 (tp) REVERT: B 202 LEU cc_start: 0.7561 (mm) cc_final: 0.7125 (tp) REVERT: B 207 VAL cc_start: 0.8909 (t) cc_final: 0.8551 (p) REVERT: B 212 GLU cc_start: 0.8219 (tp30) cc_final: 0.7934 (tp30) REVERT: B 213 GLU cc_start: 0.8195 (tt0) cc_final: 0.7702 (tt0) REVERT: B 215 CYS cc_start: 0.8310 (t) cc_final: 0.7889 (t) REVERT: B 218 ARG cc_start: 0.8869 (mmm160) cc_final: 0.8639 (mtp-110) REVERT: B 219 ILE cc_start: 0.8967 (pt) cc_final: 0.8512 (mp) REVERT: B 228 LYS cc_start: 0.8502 (ttpt) cc_final: 0.7928 (ttpt) REVERT: B 244 ILE cc_start: 0.9056 (mt) cc_final: 0.8641 (tp) REVERT: B 246 HIS cc_start: 0.8341 (m-70) cc_final: 0.8103 (m-70) REVERT: B 247 MET cc_start: 0.7424 (tmm) cc_final: 0.6091 (tmm) REVERT: B 298 ARG cc_start: 0.8546 (mmm160) cc_final: 0.7710 (mpt180) REVERT: B 305 LYS cc_start: 0.8692 (tttt) cc_final: 0.8226 (ttpp) REVERT: B 308 LEU cc_start: 0.8580 (mt) cc_final: 0.8302 (mm) REVERT: B 311 ARG cc_start: 0.8341 (ptt180) cc_final: 0.7612 (ptt-90) REVERT: B 317 MET cc_start: 0.8739 (tpp) cc_final: 0.8414 (tpp) REVERT: B 321 GLN cc_start: 0.7937 (tt0) cc_final: 0.7543 (tt0) REVERT: B 322 LEU cc_start: 0.8387 (tt) cc_final: 0.8145 (tt) REVERT: B 326 ILE cc_start: 0.8044 (mm) cc_final: 0.7753 (mm) REVERT: B 341 ARG cc_start: 0.8719 (ptt90) cc_final: 0.8325 (ptm-80) REVERT: B 351 TYR cc_start: 0.7989 (t80) cc_final: 0.7327 (t80) REVERT: B 355 GLN cc_start: 0.8641 (mt0) cc_final: 0.8344 (mt0) REVERT: B 387 THR cc_start: 0.8417 (m) cc_final: 0.8159 (m) REVERT: B 391 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7080 (mt-10) REVERT: B 635 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7431 (mt-10) REVERT: M 17 GLU cc_start: 0.7611 (pt0) cc_final: 0.7348 (pt0) REVERT: M 21 LYS cc_start: 0.7915 (mttt) cc_final: 0.7154 (mttp) REVERT: M 26 GLN cc_start: 0.8349 (mt0) cc_final: 0.7894 (tp40) REVERT: M 29 CYS cc_start: 0.8601 (t) cc_final: 0.8151 (t) REVERT: M 34 GLU cc_start: 0.8973 (tt0) cc_final: 0.8725 (tt0) REVERT: M 43 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7407 (mt-10) REVERT: M 56 LEU cc_start: 0.8341 (mp) cc_final: 0.8052 (mm) REVERT: M 71 GLN cc_start: 0.8402 (tp40) cc_final: 0.8182 (tp-100) REVERT: M 74 VAL cc_start: 0.8891 (t) cc_final: 0.8480 (p) REVERT: M 78 PHE cc_start: 0.8788 (t80) cc_final: 0.8473 (t80) REVERT: M 88 ASP cc_start: 0.8537 (m-30) cc_final: 0.8292 (m-30) REVERT: M 89 THR cc_start: 0.8900 (m) cc_final: 0.8486 (p) REVERT: M 92 ASP cc_start: 0.7824 (t0) cc_final: 0.7585 (t0) REVERT: M 116 MET cc_start: 0.7756 (mtm) cc_final: 0.7164 (mtm) REVERT: M 119 ASN cc_start: 0.8476 (t0) cc_final: 0.7899 (t0) REVERT: M 126 GLU cc_start: 0.8135 (tp30) cc_final: 0.7504 (tp30) REVERT: M 128 ASN cc_start: 0.8321 (m-40) cc_final: 0.7899 (m110) REVERT: M 131 LYS cc_start: 0.8339 (mtmm) cc_final: 0.7994 (mttp) REVERT: M 134 ILE cc_start: 0.7959 (mt) cc_final: 0.7400 (mt) REVERT: M 135 LYS cc_start: 0.8807 (mmtt) cc_final: 0.8246 (mmtt) REVERT: M 157 LEU cc_start: 0.8421 (mt) cc_final: 0.8111 (pp) REVERT: M 159 THR cc_start: 0.8144 (m) cc_final: 0.7890 (p) REVERT: M 161 GLN cc_start: 0.8238 (tp40) cc_final: 0.7980 (tp-100) REVERT: M 173 LYS cc_start: 0.7801 (tttt) cc_final: 0.7514 (tttt) REVERT: M 174 TYR cc_start: 0.7259 (m-80) cc_final: 0.6972 (m-80) REVERT: M 180 TYR cc_start: 0.6778 (m-10) cc_final: 0.6570 (m-10) REVERT: M 183 VAL cc_start: 0.8460 (t) cc_final: 0.8159 (p) REVERT: M 203 GLN cc_start: 0.7121 (mm-40) cc_final: 0.6771 (mm-40) REVERT: M 209 CYS cc_start: 0.7472 (t) cc_final: 0.7118 (t) REVERT: M 220 LEU cc_start: 0.8152 (mm) cc_final: 0.7753 (mm) REVERT: M 227 LEU cc_start: 0.8989 (mt) cc_final: 0.8496 (mp) REVERT: M 234 HIS cc_start: 0.7748 (t-90) cc_final: 0.7325 (t-90) REVERT: M 239 PHE cc_start: 0.7794 (p90) cc_final: 0.7588 (p90) REVERT: M 240 LYS cc_start: 0.8540 (mttt) cc_final: 0.8095 (mttt) REVERT: M 242 TRP cc_start: 0.7253 (t-100) cc_final: 0.6957 (t-100) REVERT: M 257 PHE cc_start: 0.8449 (p90) cc_final: 0.8093 (p90) REVERT: M 258 ARG cc_start: 0.8181 (mtm180) cc_final: 0.7941 (mtm-85) REVERT: M 262 TYR cc_start: 0.8363 (p90) cc_final: 0.8002 (p90) REVERT: M 298 LYS cc_start: 0.8894 (tttt) cc_final: 0.8506 (tttt) REVERT: M 300 ASN cc_start: 0.8933 (p0) cc_final: 0.8710 (p0) REVERT: M 377 PHE cc_start: 0.8016 (p90) cc_final: 0.7602 (p90) REVERT: M 388 LYS cc_start: 0.8791 (mppt) cc_final: 0.8522 (mppt) REVERT: M 393 ASP cc_start: 0.8146 (t0) cc_final: 0.7739 (t0) REVERT: M 402 PHE cc_start: 0.7631 (m-80) cc_final: 0.7160 (m-80) REVERT: M 414 PHE cc_start: 0.7794 (t80) cc_final: 0.7203 (t80) REVERT: C 21 LEU cc_start: 0.8393 (tp) cc_final: 0.8118 (tp) REVERT: C 23 VAL cc_start: 0.8716 (m) cc_final: 0.7939 (m) REVERT: C 37 LEU cc_start: 0.8900 (mt) cc_final: 0.8642 (mt) REVERT: C 58 TYR cc_start: 0.7931 (t80) cc_final: 0.7497 (t80) REVERT: C 64 THR cc_start: 0.6756 (m) cc_final: 0.6509 (t) REVERT: C 78 TRP cc_start: 0.8134 (m-10) cc_final: 0.7279 (m-10) REVERT: C 81 TYR cc_start: 0.7174 (m-80) cc_final: 0.6580 (m-80) REVERT: C 82 PHE cc_start: 0.7848 (m-10) cc_final: 0.7348 (m-80) REVERT: C 84 ASN cc_start: 0.8431 (t0) cc_final: 0.7746 (t0) REVERT: C 86 GLN cc_start: 0.7842 (mm-40) cc_final: 0.6578 (mt0) REVERT: C 99 ARG cc_start: 0.8100 (mtp180) cc_final: 0.7891 (mtp-110) REVERT: C 110 MET cc_start: 0.8353 (mmm) cc_final: 0.7850 (mmm) REVERT: C 115 GLU cc_start: 0.8159 (tt0) cc_final: 0.7935 (tt0) REVERT: C 116 LEU cc_start: 0.7990 (mt) cc_final: 0.7787 (mt) REVERT: C 128 GLN cc_start: 0.7202 (mm-40) cc_final: 0.6400 (mm-40) REVERT: C 143 LEU cc_start: 0.8830 (mt) cc_final: 0.8571 (mt) REVERT: C 145 LEU cc_start: 0.8229 (mt) cc_final: 0.7962 (mt) REVERT: C 153 TRP cc_start: 0.8511 (p-90) cc_final: 0.8074 (p-90) REVERT: C 159 CYS cc_start: 0.8221 (t) cc_final: 0.7855 (t) REVERT: C 167 TYR cc_start: 0.7880 (m-10) cc_final: 0.7084 (m-10) REVERT: C 168 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7775 (mt-10) REVERT: C 171 ASP cc_start: 0.8306 (m-30) cc_final: 0.7931 (m-30) REVERT: C 172 TRP cc_start: 0.8247 (t60) cc_final: 0.7362 (t60) REVERT: C 176 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7562 (mm-40) REVERT: b 43 LYS cc_start: 0.8247 (mttt) cc_final: 0.7773 (tttp) REVERT: b 47 LEU cc_start: 0.8963 (mt) cc_final: 0.8612 (mt) REVERT: b 50 MET cc_start: 0.8493 (mtm) cc_final: 0.8170 (mtm) REVERT: b 54 ASN cc_start: 0.7521 (p0) cc_final: 0.7202 (t0) REVERT: b 55 LYS cc_start: 0.8461 (ttpt) cc_final: 0.8043 (mtpt) REVERT: b 63 MET cc_start: 0.8568 (mmm) cc_final: 0.7616 (mmm) REVERT: b 66 ILE cc_start: 0.8542 (mm) cc_final: 0.8305 (mm) REVERT: b 72 LYS cc_start: 0.8791 (mmtt) cc_final: 0.8245 (mtpt) REVERT: b 80 PHE cc_start: 0.8524 (t80) cc_final: 0.7747 (t80) REVERT: b 85 LYS cc_start: 0.8634 (mttt) cc_final: 0.8415 (mttt) REVERT: b 98 VAL cc_start: 0.8873 (t) cc_final: 0.8201 (t) REVERT: b 101 TYR cc_start: 0.8632 (t80) cc_final: 0.8354 (t80) REVERT: b 112 LEU cc_start: 0.8073 (mp) cc_final: 0.6939 (mp) REVERT: b 121 GLN cc_start: 0.8108 (tt0) cc_final: 0.7820 (mt0) REVERT: b 132 ARG cc_start: 0.8470 (mtt180) cc_final: 0.8267 (mtm-85) REVERT: b 139 LEU cc_start: 0.8343 (tp) cc_final: 0.8061 (tt) REVERT: b 141 SER cc_start: 0.8456 (m) cc_final: 0.8093 (m) REVERT: b 142 ILE cc_start: 0.9014 (mm) cc_final: 0.8656 (mp) REVERT: b 147 ILE cc_start: 0.8449 (pt) cc_final: 0.8242 (pt) REVERT: b 150 ILE cc_start: 0.8086 (mt) cc_final: 0.7718 (mt) REVERT: b 151 MET cc_start: 0.7625 (mtp) cc_final: 0.7202 (mtp) REVERT: b 152 MET cc_start: 0.8117 (tpt) cc_final: 0.7859 (tpt) REVERT: b 155 ILE cc_start: 0.9226 (mm) cc_final: 0.9018 (mm) REVERT: b 181 ASP cc_start: 0.8196 (t0) cc_final: 0.7724 (t0) REVERT: b 186 GLU cc_start: 0.8286 (pm20) cc_final: 0.7915 (pm20) REVERT: b 187 MET cc_start: 0.8325 (mtm) cc_final: 0.7709 (mtm) REVERT: b 191 VAL cc_start: 0.8948 (t) cc_final: 0.8699 (p) REVERT: b 195 LEU cc_start: 0.9032 (mt) cc_final: 0.8711 (mt) REVERT: b 196 LEU cc_start: 0.8656 (mt) cc_final: 0.8276 (tp) REVERT: b 202 LEU cc_start: 0.7614 (mm) cc_final: 0.7174 (tp) REVERT: b 207 VAL cc_start: 0.8906 (t) cc_final: 0.8472 (p) REVERT: b 212 GLU cc_start: 0.8251 (tp30) cc_final: 0.8002 (tp30) REVERT: b 215 CYS cc_start: 0.8399 (t) cc_final: 0.7959 (t) REVERT: b 219 ILE cc_start: 0.9044 (pt) cc_final: 0.8131 (mp) REVERT: b 228 LYS cc_start: 0.8538 (ttpt) cc_final: 0.8009 (ttpt) REVERT: b 244 ILE cc_start: 0.9068 (mt) cc_final: 0.8822 (tp) REVERT: b 247 MET cc_start: 0.7501 (tmm) cc_final: 0.6966 (tmm) REVERT: b 298 ARG cc_start: 0.8774 (mmm160) cc_final: 0.7465 (mpt180) REVERT: b 305 LYS cc_start: 0.8623 (tttt) cc_final: 0.8347 (ttpp) REVERT: b 307 LEU cc_start: 0.8929 (mt) cc_final: 0.8688 (mm) REVERT: b 308 LEU cc_start: 0.8689 (mt) cc_final: 0.8356 (mm) REVERT: b 311 ARG cc_start: 0.8395 (ptt180) cc_final: 0.7675 (ptt-90) REVERT: b 317 MET cc_start: 0.8779 (tpp) cc_final: 0.8535 (tpt) REVERT: b 321 GLN cc_start: 0.7925 (tt0) cc_final: 0.7486 (tt0) REVERT: b 322 LEU cc_start: 0.8487 (tt) cc_final: 0.8211 (tt) REVERT: b 324 TRP cc_start: 0.8670 (t-100) cc_final: 0.8031 (t-100) REVERT: b 326 ILE cc_start: 0.8095 (mm) cc_final: 0.7893 (mm) REVERT: b 360 MET cc_start: 0.8296 (ttm) cc_final: 0.6718 (ttm) REVERT: b 417 ASP cc_start: 0.7714 (t0) cc_final: 0.7358 (m-30) REVERT: b 645 ASP cc_start: 0.7733 (t0) cc_final: 0.7256 (t70) REVERT: m 1 MET cc_start: 0.6940 (mtt) cc_final: 0.6423 (mtt) REVERT: m 17 GLU cc_start: 0.7358 (pt0) cc_final: 0.7129 (pt0) REVERT: m 29 CYS cc_start: 0.8367 (m) cc_final: 0.7860 (t) REVERT: m 33 PHE cc_start: 0.8557 (m-80) cc_final: 0.8096 (m-80) REVERT: m 36 GLN cc_start: 0.8410 (tp40) cc_final: 0.8005 (tp40) REVERT: m 43 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7461 (mt-10) REVERT: m 71 GLN cc_start: 0.8370 (tp40) cc_final: 0.7668 (tp40) REVERT: m 78 PHE cc_start: 0.8743 (t80) cc_final: 0.8262 (t80) REVERT: m 81 GLU cc_start: 0.7730 (tp30) cc_final: 0.7413 (tp30) REVERT: m 89 THR cc_start: 0.8943 (m) cc_final: 0.8735 (m) REVERT: m 103 LYS cc_start: 0.7292 (mtmm) cc_final: 0.6975 (mtmm) REVERT: m 108 ILE cc_start: 0.8760 (mt) cc_final: 0.8542 (mm) REVERT: m 115 GLU cc_start: 0.8404 (tp30) cc_final: 0.7736 (tp30) REVERT: m 116 MET cc_start: 0.7652 (mtm) cc_final: 0.7374 (mtm) REVERT: m 119 ASN cc_start: 0.8439 (t0) cc_final: 0.8139 (t0) REVERT: m 126 GLU cc_start: 0.8180 (tp30) cc_final: 0.7557 (tp30) REVERT: m 128 ASN cc_start: 0.8384 (m-40) cc_final: 0.7678 (m-40) REVERT: m 131 LYS cc_start: 0.8377 (mtmm) cc_final: 0.7776 (mtmt) REVERT: m 134 ILE cc_start: 0.8129 (mt) cc_final: 0.7602 (tp) REVERT: m 140 LEU cc_start: 0.8460 (mt) cc_final: 0.8244 (tt) REVERT: m 141 ARG cc_start: 0.8171 (mmt90) cc_final: 0.7753 (mmt90) REVERT: m 173 LYS cc_start: 0.8099 (tttt) cc_final: 0.7795 (tttt) REVERT: m 209 CYS cc_start: 0.7367 (t) cc_final: 0.6325 (m) REVERT: m 210 ILE cc_start: 0.8673 (mm) cc_final: 0.8470 (mm) REVERT: m 220 LEU cc_start: 0.7973 (mm) cc_final: 0.7553 (mm) REVERT: m 227 LEU cc_start: 0.9034 (mm) cc_final: 0.8823 (mp) REVERT: m 234 HIS cc_start: 0.7794 (t-90) cc_final: 0.7405 (t-90) REVERT: m 240 LYS cc_start: 0.8631 (mttt) cc_final: 0.8043 (mmmm) REVERT: m 257 PHE cc_start: 0.8498 (p90) cc_final: 0.8160 (p90) REVERT: m 272 ILE cc_start: 0.7526 (mm) cc_final: 0.6783 (mm) REVERT: m 274 VAL cc_start: 0.7864 (t) cc_final: 0.7534 (p) REVERT: m 293 ILE cc_start: 0.7705 (mm) cc_final: 0.7456 (mm) REVERT: m 298 LYS cc_start: 0.8977 (tttt) cc_final: 0.8585 (tttt) REVERT: m 300 ASN cc_start: 0.8988 (p0) cc_final: 0.8779 (p0) REVERT: m 377 PHE cc_start: 0.7874 (p90) cc_final: 0.7457 (p90) REVERT: m 393 ASP cc_start: 0.7951 (t0) cc_final: 0.7710 (t0) REVERT: m 400 LYS cc_start: 0.8879 (mmtm) cc_final: 0.8600 (mmtt) REVERT: m 414 PHE cc_start: 0.7898 (t80) cc_final: 0.7229 (t80) REVERT: c 45 THR cc_start: 0.9040 (p) cc_final: 0.8603 (t) REVERT: c 53 VAL cc_start: 0.8420 (p) cc_final: 0.8137 (m) REVERT: c 58 TYR cc_start: 0.8026 (t80) cc_final: 0.7396 (t80) REVERT: c 64 THR cc_start: 0.6729 (m) cc_final: 0.6329 (t) REVERT: c 78 TRP cc_start: 0.8198 (m-10) cc_final: 0.7417 (m-10) REVERT: c 79 ARG cc_start: 0.8735 (ptm-80) cc_final: 0.8296 (mtm110) REVERT: c 82 PHE cc_start: 0.8095 (m-80) cc_final: 0.7830 (m-80) REVERT: c 84 ASN cc_start: 0.8098 (t0) cc_final: 0.7173 (t0) REVERT: c 86 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7200 (mm-40) REVERT: c 95 ASN cc_start: 0.7658 (t160) cc_final: 0.7191 (t0) REVERT: c 110 MET cc_start: 0.8370 (mmm) cc_final: 0.7834 (mmm) REVERT: c 115 GLU cc_start: 0.7695 (tt0) cc_final: 0.7389 (tt0) REVERT: c 128 GLN cc_start: 0.7395 (mm-40) cc_final: 0.7097 (mm-40) REVERT: c 151 ARG cc_start: 0.8297 (ttm-80) cc_final: 0.8037 (ttt-90) REVERT: c 153 TRP cc_start: 0.8560 (p-90) cc_final: 0.8249 (p-90) REVERT: c 159 CYS cc_start: 0.8445 (t) cc_final: 0.8062 (t) REVERT: c 167 TYR cc_start: 0.7937 (m-10) cc_final: 0.7243 (m-10) REVERT: c 168 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7806 (mt-10) REVERT: c 171 ASP cc_start: 0.8360 (m-30) cc_final: 0.7982 (m-30) outliers start: 1 outliers final: 1 residues processed: 808 average time/residue: 0.1375 time to fit residues: 158.5351 Evaluate side-chains 764 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 763 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 38 optimal weight: 0.7980 chunk 134 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 166 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 26 GLN m 54 HIS ** m 177 ASN ** 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 = 0.3804 r_free = 0.3804 target = 0.139968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.115320 restraints weight = 30908.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119606 restraints weight = 16671.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.122536 restraints weight = 10417.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.124511 restraints weight = 7212.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.126042 restraints weight = 5395.947| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16108 Z= 0.162 Angle : 0.588 7.735 21822 Z= 0.312 Chirality : 0.045 0.170 2524 Planarity : 0.004 0.051 2752 Dihedral : 10.314 169.322 2154 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.20), residues: 1954 helix: 1.10 (0.18), residues: 818 sheet: 0.25 (0.27), residues: 370 loop : 1.23 (0.25), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 167 TYR 0.017 0.002 TYR c 58 PHE 0.023 0.002 PHE m 121 TRP 0.028 0.002 TRP C 66 HIS 0.003 0.001 HIS M 54 Details of bonding type rmsd covalent geometry : bond 0.00319 (16108) covalent geometry : angle 0.58796 (21822) hydrogen bonds : bond 0.04557 ( 815) hydrogen bonds : angle 5.26984 ( 2361) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 786 time to evaluate : 0.720 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: B 43 LYS cc_start: 0.8230 (mttt) cc_final: 0.7591 (mmmt) REVERT: B 47 LEU cc_start: 0.8986 (mt) cc_final: 0.8537 (mt) REVERT: B 50 MET cc_start: 0.8597 (mtm) cc_final: 0.8133 (mtm) REVERT: B 51 LEU cc_start: 0.8728 (mt) cc_final: 0.8445 (mt) REVERT: B 52 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7591 (mm-30) REVERT: B 54 ASN cc_start: 0.7943 (m110) cc_final: 0.7424 (m110) REVERT: B 63 MET cc_start: 0.8501 (mmm) cc_final: 0.7727 (mmm) REVERT: B 66 ILE cc_start: 0.8609 (mm) cc_final: 0.8342 (mm) REVERT: B 72 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8405 (mtpt) REVERT: B 74 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8373 (mmtt) REVERT: B 79 LEU cc_start: 0.8644 (mt) cc_final: 0.8402 (mt) REVERT: B 80 PHE cc_start: 0.8404 (t80) cc_final: 0.7537 (t80) REVERT: B 84 VAL cc_start: 0.8579 (p) cc_final: 0.8279 (m) REVERT: B 85 LYS cc_start: 0.8601 (mttt) cc_final: 0.7871 (mttt) REVERT: B 90 LYS cc_start: 0.8401 (mttt) cc_final: 0.8140 (mttt) REVERT: B 94 ILE cc_start: 0.8299 (mt) cc_final: 0.8049 (mm) REVERT: B 98 VAL cc_start: 0.8669 (t) cc_final: 0.8115 (t) REVERT: B 101 TYR cc_start: 0.8655 (t80) cc_final: 0.8391 (t80) REVERT: B 102 LEU cc_start: 0.8961 (tt) cc_final: 0.8759 (tt) REVERT: B 104 ARG cc_start: 0.8722 (tpt90) cc_final: 0.8278 (tpt90) REVERT: B 112 LEU cc_start: 0.8171 (mt) cc_final: 0.7565 (mp) REVERT: B 125 LYS cc_start: 0.8853 (mttt) cc_final: 0.8348 (mtpp) REVERT: B 132 ARG cc_start: 0.8379 (mtt180) cc_final: 0.8035 (mtm180) REVERT: B 141 SER cc_start: 0.8508 (m) cc_final: 0.8040 (p) REVERT: B 147 ILE cc_start: 0.8521 (pt) cc_final: 0.8281 (pt) REVERT: B 151 MET cc_start: 0.7731 (mtp) cc_final: 0.7314 (mtp) REVERT: B 152 MET cc_start: 0.8075 (tpt) cc_final: 0.7787 (tpt) REVERT: B 155 ILE cc_start: 0.9222 (mm) cc_final: 0.9019 (mm) REVERT: B 169 ASN cc_start: 0.8649 (m-40) cc_final: 0.8422 (m-40) REVERT: B 175 GLN cc_start: 0.8503 (tm-30) cc_final: 0.8020 (tm-30) REVERT: B 183 GLU cc_start: 0.8550 (mp0) cc_final: 0.8347 (mp0) REVERT: B 185 LYS cc_start: 0.8425 (pttp) cc_final: 0.8173 (pttp) REVERT: B 190 GLU cc_start: 0.8145 (tt0) cc_final: 0.7943 (tt0) REVERT: B 191 VAL cc_start: 0.9013 (t) cc_final: 0.8812 (p) REVERT: B 193 GLU cc_start: 0.8368 (tt0) cc_final: 0.8093 (tt0) REVERT: B 195 LEU cc_start: 0.9051 (mm) cc_final: 0.8580 (mt) REVERT: B 196 LEU cc_start: 0.8739 (mt) cc_final: 0.8422 (tp) REVERT: B 202 LEU cc_start: 0.7532 (mm) cc_final: 0.7074 (tp) REVERT: B 207 VAL cc_start: 0.8851 (t) cc_final: 0.8486 (p) REVERT: B 213 GLU cc_start: 0.8075 (tt0) cc_final: 0.7704 (tt0) REVERT: B 215 CYS cc_start: 0.8312 (t) cc_final: 0.7898 (t) REVERT: B 218 ARG cc_start: 0.8934 (mmm160) cc_final: 0.8709 (mtp-110) REVERT: B 228 LYS cc_start: 0.8591 (ttpt) cc_final: 0.8041 (ttpt) REVERT: B 244 ILE cc_start: 0.9037 (mt) cc_final: 0.8487 (tp) REVERT: B 246 HIS cc_start: 0.8484 (m-70) cc_final: 0.8111 (m-70) REVERT: B 247 MET cc_start: 0.7256 (tmm) cc_final: 0.6756 (tmm) REVERT: B 298 ARG cc_start: 0.8620 (mmm160) cc_final: 0.7757 (mpt180) REVERT: B 305 LYS cc_start: 0.8716 (tttt) cc_final: 0.8287 (ttpp) REVERT: B 308 LEU cc_start: 0.8591 (mt) cc_final: 0.8309 (mm) REVERT: B 311 ARG cc_start: 0.8362 (ptt180) cc_final: 0.7682 (ptt-90) REVERT: B 317 MET cc_start: 0.8702 (tpp) cc_final: 0.8389 (tpp) REVERT: B 321 GLN cc_start: 0.8073 (tt0) cc_final: 0.7631 (tt0) REVERT: B 326 ILE cc_start: 0.8095 (mm) cc_final: 0.7792 (mm) REVERT: B 341 ARG cc_start: 0.8716 (ptt90) cc_final: 0.8286 (ptm-80) REVERT: B 387 THR cc_start: 0.8382 (m) cc_final: 0.8089 (m) REVERT: B 388 LEU cc_start: 0.8669 (mm) cc_final: 0.8418 (mm) REVERT: B 391 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7111 (mt-10) REVERT: B 417 ASP cc_start: 0.8187 (t0) cc_final: 0.7371 (m-30) REVERT: B 635 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7559 (mt-10) REVERT: M 14 ILE cc_start: 0.7890 (mt) cc_final: 0.7047 (mt) REVERT: M 17 GLU cc_start: 0.7651 (pt0) cc_final: 0.7326 (pt0) REVERT: M 21 LYS cc_start: 0.8010 (mttt) cc_final: 0.7288 (mttp) REVERT: M 26 GLN cc_start: 0.8353 (mt0) cc_final: 0.8044 (mm-40) REVERT: M 29 CYS cc_start: 0.8636 (t) cc_final: 0.8252 (t) REVERT: M 34 GLU cc_start: 0.9001 (tt0) cc_final: 0.8742 (tt0) REVERT: M 43 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7443 (mt-10) REVERT: M 49 ILE cc_start: 0.8407 (mt) cc_final: 0.8183 (mp) REVERT: M 56 LEU cc_start: 0.8342 (mp) cc_final: 0.8003 (mm) REVERT: M 78 PHE cc_start: 0.8762 (t80) cc_final: 0.8515 (t80) REVERT: M 80 ILE cc_start: 0.8596 (mt) cc_final: 0.8280 (mm) REVERT: M 88 ASP cc_start: 0.8469 (m-30) cc_final: 0.8189 (m-30) REVERT: M 89 THR cc_start: 0.9022 (m) cc_final: 0.8688 (p) REVERT: M 108 ILE cc_start: 0.8894 (mt) cc_final: 0.8428 (mm) REVERT: M 116 MET cc_start: 0.7801 (mtm) cc_final: 0.7309 (mtm) REVERT: M 119 ASN cc_start: 0.8228 (t0) cc_final: 0.7622 (t0) REVERT: M 126 GLU cc_start: 0.8184 (tp30) cc_final: 0.7401 (tp30) REVERT: M 128 ASN cc_start: 0.8306 (m-40) cc_final: 0.7909 (m-40) REVERT: M 129 ILE cc_start: 0.8849 (mm) cc_final: 0.8577 (tp) REVERT: M 131 LYS cc_start: 0.8485 (mtmm) cc_final: 0.7921 (mttp) REVERT: M 134 ILE cc_start: 0.8347 (mt) cc_final: 0.7945 (mm) REVERT: M 135 LYS cc_start: 0.8915 (mmtt) cc_final: 0.8376 (mmtt) REVERT: M 157 LEU cc_start: 0.8522 (mt) cc_final: 0.8200 (pp) REVERT: M 159 THR cc_start: 0.8166 (m) cc_final: 0.7794 (t) REVERT: M 161 GLN cc_start: 0.8289 (tp40) cc_final: 0.8084 (tp-100) REVERT: M 173 LYS cc_start: 0.7938 (tttt) cc_final: 0.7665 (tttt) REVERT: M 174 TYR cc_start: 0.7632 (m-80) cc_final: 0.7225 (m-80) REVERT: M 183 VAL cc_start: 0.8454 (t) cc_final: 0.8219 (p) REVERT: M 220 LEU cc_start: 0.8210 (mm) cc_final: 0.7816 (mm) REVERT: M 227 LEU cc_start: 0.8980 (mt) cc_final: 0.8542 (mp) REVERT: M 234 HIS cc_start: 0.7891 (t-90) cc_final: 0.7535 (t-90) REVERT: M 240 LYS cc_start: 0.8479 (mttt) cc_final: 0.7981 (mttt) REVERT: M 242 TRP cc_start: 0.7551 (t-100) cc_final: 0.7148 (t-100) REVERT: M 245 GLU cc_start: 0.6865 (mm-30) cc_final: 0.6326 (mm-30) REVERT: M 257 PHE cc_start: 0.8471 (p90) cc_final: 0.8193 (p90) REVERT: M 262 TYR cc_start: 0.8418 (p90) cc_final: 0.8035 (p90) REVERT: M 298 LYS cc_start: 0.8987 (tttt) cc_final: 0.8531 (tttt) REVERT: M 299 GLN cc_start: 0.8009 (mt0) cc_final: 0.6630 (mt0) REVERT: M 393 ASP cc_start: 0.7969 (t0) cc_final: 0.7477 (t0) REVERT: M 402 PHE cc_start: 0.7737 (m-80) cc_final: 0.7254 (m-10) REVERT: M 414 PHE cc_start: 0.7900 (t80) cc_final: 0.7373 (t80) REVERT: C 18 MET cc_start: 0.6570 (mmm) cc_final: 0.6306 (mmm) REVERT: C 37 LEU cc_start: 0.8894 (mt) cc_final: 0.8634 (mt) REVERT: C 51 PHE cc_start: 0.7768 (p90) cc_final: 0.7541 (p90) REVERT: C 58 TYR cc_start: 0.8095 (t80) cc_final: 0.7695 (t80) REVERT: C 64 THR cc_start: 0.6700 (m) cc_final: 0.6436 (t) REVERT: C 78 TRP cc_start: 0.8145 (m-10) cc_final: 0.7477 (m-10) REVERT: C 79 ARG cc_start: 0.8834 (ptm-80) cc_final: 0.8618 (ptm-80) REVERT: C 81 TYR cc_start: 0.7086 (m-80) cc_final: 0.6293 (m-80) REVERT: C 82 PHE cc_start: 0.7871 (m-10) cc_final: 0.7349 (m-80) REVERT: C 84 ASN cc_start: 0.8437 (t0) cc_final: 0.7682 (t0) REVERT: C 86 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7179 (mt0) REVERT: C 110 MET cc_start: 0.8326 (mmm) cc_final: 0.7835 (mmm) REVERT: C 115 GLU cc_start: 0.8268 (tt0) cc_final: 0.7942 (tt0) REVERT: C 116 LEU cc_start: 0.7938 (mt) cc_final: 0.7546 (mt) REVERT: C 142 LYS cc_start: 0.8929 (mttm) cc_final: 0.8596 (mttm) REVERT: C 145 LEU cc_start: 0.8234 (mt) cc_final: 0.7873 (mt) REVERT: C 151 ARG cc_start: 0.8672 (tpp-160) cc_final: 0.8460 (mmt180) REVERT: C 153 TRP cc_start: 0.8571 (p-90) cc_final: 0.7990 (p-90) REVERT: C 167 TYR cc_start: 0.7973 (m-10) cc_final: 0.7177 (m-10) REVERT: C 168 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7725 (mt-10) REVERT: C 171 ASP cc_start: 0.8331 (m-30) cc_final: 0.7894 (m-30) REVERT: b 43 LYS cc_start: 0.8160 (mttt) cc_final: 0.7756 (tttp) REVERT: b 47 LEU cc_start: 0.8959 (mt) cc_final: 0.8554 (mt) REVERT: b 48 LYS cc_start: 0.9001 (ptpp) cc_final: 0.8492 (ptpp) REVERT: b 49 GLN cc_start: 0.8841 (tt0) cc_final: 0.8629 (tt0) REVERT: b 50 MET cc_start: 0.8528 (mtm) cc_final: 0.8253 (mtm) REVERT: b 51 LEU cc_start: 0.8823 (mt) cc_final: 0.8483 (mt) REVERT: b 55 LYS cc_start: 0.8374 (ttpt) cc_final: 0.8068 (mtpt) REVERT: b 59 LYS cc_start: 0.8660 (mtmm) cc_final: 0.8358 (mttp) REVERT: b 63 MET cc_start: 0.8433 (mmm) cc_final: 0.7934 (mmm) REVERT: b 66 ILE cc_start: 0.8530 (mm) cc_final: 0.8204 (mm) REVERT: b 72 LYS cc_start: 0.8833 (mmtt) cc_final: 0.8304 (mtmt) REVERT: b 79 LEU cc_start: 0.8545 (mt) cc_final: 0.8335 (mt) REVERT: b 80 PHE cc_start: 0.8511 (t80) cc_final: 0.7770 (t80) REVERT: b 85 LYS cc_start: 0.8543 (mttt) cc_final: 0.8231 (mttt) REVERT: b 112 LEU cc_start: 0.8076 (mp) cc_final: 0.7073 (mp) REVERT: b 132 ARG cc_start: 0.8494 (mtt180) cc_final: 0.8157 (mtm180) REVERT: b 141 SER cc_start: 0.8537 (m) cc_final: 0.8264 (m) REVERT: b 142 ILE cc_start: 0.9040 (mm) cc_final: 0.8710 (mp) REVERT: b 150 ILE cc_start: 0.8151 (mt) cc_final: 0.7927 (mt) REVERT: b 151 MET cc_start: 0.7586 (mtp) cc_final: 0.7147 (mtp) REVERT: b 152 MET cc_start: 0.8068 (tpt) cc_final: 0.7814 (tpt) REVERT: b 155 ILE cc_start: 0.9236 (mm) cc_final: 0.9024 (mm) REVERT: b 175 GLN cc_start: 0.8689 (tm-30) cc_final: 0.8140 (tm-30) REVERT: b 181 ASP cc_start: 0.8327 (t0) cc_final: 0.7938 (t0) REVERT: b 186 GLU cc_start: 0.8312 (pm20) cc_final: 0.7906 (pm20) REVERT: b 187 MET cc_start: 0.8353 (mtm) cc_final: 0.7831 (mtm) REVERT: b 193 GLU cc_start: 0.8421 (tt0) cc_final: 0.8095 (tt0) REVERT: b 195 LEU cc_start: 0.9065 (mt) cc_final: 0.8739 (mt) REVERT: b 196 LEU cc_start: 0.8808 (mt) cc_final: 0.8434 (tp) REVERT: b 202 LEU cc_start: 0.7678 (mm) cc_final: 0.7270 (tp) REVERT: b 207 VAL cc_start: 0.8892 (t) cc_final: 0.8442 (p) REVERT: b 212 GLU cc_start: 0.7980 (tp30) cc_final: 0.7754 (tp30) REVERT: b 213 GLU cc_start: 0.8247 (tt0) cc_final: 0.7794 (tt0) REVERT: b 215 CYS cc_start: 0.8362 (t) cc_final: 0.7718 (t) REVERT: b 218 ARG cc_start: 0.9001 (mmm160) cc_final: 0.8745 (mmm160) REVERT: b 228 LYS cc_start: 0.8560 (ttpt) cc_final: 0.8036 (ttpt) REVERT: b 244 ILE cc_start: 0.9104 (mt) cc_final: 0.8703 (tp) REVERT: b 247 MET cc_start: 0.7321 (tmm) cc_final: 0.5922 (tmm) REVERT: b 248 LEU cc_start: 0.8357 (mt) cc_final: 0.8151 (mm) REVERT: b 298 ARG cc_start: 0.8792 (mmm160) cc_final: 0.7448 (mpt180) REVERT: b 307 LEU cc_start: 0.8960 (mt) cc_final: 0.8573 (mt) REVERT: b 308 LEU cc_start: 0.8718 (mt) cc_final: 0.8359 (mm) REVERT: b 311 ARG cc_start: 0.8378 (ptt180) cc_final: 0.7734 (ptt-90) REVERT: b 317 MET cc_start: 0.8717 (tpp) cc_final: 0.8460 (tpt) REVERT: b 321 GLN cc_start: 0.7980 (tt0) cc_final: 0.7539 (tt0) REVERT: b 322 LEU cc_start: 0.8474 (tt) cc_final: 0.8223 (tt) REVERT: b 324 TRP cc_start: 0.8679 (t-100) cc_final: 0.7928 (t-100) REVERT: b 326 ILE cc_start: 0.8113 (mm) cc_final: 0.7838 (mm) REVERT: b 331 GLU cc_start: 0.7121 (mp0) cc_final: 0.6776 (mp0) REVERT: b 351 TYR cc_start: 0.7995 (t80) cc_final: 0.7776 (t80) REVERT: b 355 GLN cc_start: 0.8577 (mt0) cc_final: 0.8328 (mt0) REVERT: b 360 MET cc_start: 0.8409 (ttm) cc_final: 0.6253 (ttm) REVERT: b 384 MET cc_start: 0.7871 (ptt) cc_final: 0.7325 (ptt) REVERT: b 417 ASP cc_start: 0.7809 (t0) cc_final: 0.7514 (t0) REVERT: b 627 ASN cc_start: 0.8615 (m110) cc_final: 0.8415 (m-40) REVERT: m 1 MET cc_start: 0.6908 (mtt) cc_final: 0.6468 (mtt) REVERT: m 17 GLU cc_start: 0.7517 (pt0) cc_final: 0.7276 (pt0) REVERT: m 21 LYS cc_start: 0.7843 (mttt) cc_final: 0.7173 (mttm) REVERT: m 24 VAL cc_start: 0.8555 (t) cc_final: 0.8335 (p) REVERT: m 29 CYS cc_start: 0.8372 (m) cc_final: 0.7906 (t) REVERT: m 34 GLU cc_start: 0.8816 (tt0) cc_final: 0.8603 (tt0) REVERT: m 36 GLN cc_start: 0.8363 (tp40) cc_final: 0.7973 (tp40) REVERT: m 43 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7477 (mt-10) REVERT: m 44 ASN cc_start: 0.8155 (t0) cc_final: 0.7413 (t0) REVERT: m 45 VAL cc_start: 0.8864 (t) cc_final: 0.8626 (t) REVERT: m 71 GLN cc_start: 0.8377 (tp40) cc_final: 0.7809 (tp40) REVERT: m 77 LEU cc_start: 0.8559 (mt) cc_final: 0.8176 (mt) REVERT: m 78 PHE cc_start: 0.8736 (t80) cc_final: 0.8274 (t80) REVERT: m 80 ILE cc_start: 0.8570 (mt) cc_final: 0.8354 (mt) REVERT: m 81 GLU cc_start: 0.7714 (tp30) cc_final: 0.7395 (tp30) REVERT: m 88 ASP cc_start: 0.8452 (m-30) cc_final: 0.8185 (m-30) REVERT: m 89 THR cc_start: 0.8959 (m) cc_final: 0.8550 (p) REVERT: m 108 ILE cc_start: 0.8857 (mt) cc_final: 0.8504 (mm) REVERT: m 116 MET cc_start: 0.7633 (mtm) cc_final: 0.7282 (mtm) REVERT: m 119 ASN cc_start: 0.8309 (t0) cc_final: 0.7651 (t0) REVERT: m 126 GLU cc_start: 0.8226 (tp30) cc_final: 0.7585 (tp30) REVERT: m 128 ASN cc_start: 0.8269 (m-40) cc_final: 0.7567 (m-40) REVERT: m 131 LYS cc_start: 0.8405 (mtmm) cc_final: 0.7716 (mtmt) REVERT: m 134 ILE cc_start: 0.8223 (mt) cc_final: 0.7731 (tp) REVERT: m 140 LEU cc_start: 0.8487 (mt) cc_final: 0.8256 (tt) REVERT: m 141 ARG cc_start: 0.8156 (mmt90) cc_final: 0.7736 (mmt90) REVERT: m 172 VAL cc_start: 0.8795 (t) cc_final: 0.8448 (m) REVERT: m 209 CYS cc_start: 0.7398 (t) cc_final: 0.6336 (m) REVERT: m 234 HIS cc_start: 0.7978 (t-90) cc_final: 0.7750 (t-90) REVERT: m 240 LYS cc_start: 0.8614 (mttt) cc_final: 0.8068 (mmmm) REVERT: m 243 GLU cc_start: 0.8489 (tp30) cc_final: 0.8139 (tp30) REVERT: m 257 PHE cc_start: 0.8555 (p90) cc_final: 0.8204 (p90) REVERT: m 262 TYR cc_start: 0.8179 (p90) cc_final: 0.7087 (p90) REVERT: m 272 ILE cc_start: 0.7763 (mm) cc_final: 0.6678 (mp) REVERT: m 293 ILE cc_start: 0.7790 (mm) cc_final: 0.7518 (mm) REVERT: m 298 LYS cc_start: 0.9075 (tttt) cc_final: 0.8708 (tttt) REVERT: m 373 LEU cc_start: 0.7486 (tt) cc_final: 0.7268 (tt) REVERT: m 377 PHE cc_start: 0.7788 (p90) cc_final: 0.7481 (p90) REVERT: m 393 ASP cc_start: 0.8060 (t0) cc_final: 0.7660 (t0) REVERT: m 402 PHE cc_start: 0.7661 (m-80) cc_final: 0.7125 (m-10) REVERT: m 406 LYS cc_start: 0.8640 (ttmt) cc_final: 0.8158 (mtpt) REVERT: m 414 PHE cc_start: 0.7930 (t80) cc_final: 0.7466 (t80) REVERT: c 19 ARG cc_start: 0.7267 (ttm170) cc_final: 0.6290 (ttm170) REVERT: c 30 LYS cc_start: 0.8473 (mttp) cc_final: 0.8264 (mttp) REVERT: c 53 VAL cc_start: 0.8397 (p) cc_final: 0.8148 (m) REVERT: c 58 TYR cc_start: 0.8107 (t80) cc_final: 0.7576 (t80) REVERT: c 64 THR cc_start: 0.6743 (m) cc_final: 0.6372 (t) REVERT: c 68 VAL cc_start: 0.8116 (t) cc_final: 0.7866 (p) REVERT: c 78 TRP cc_start: 0.8198 (m-10) cc_final: 0.7442 (m-10) REVERT: c 79 ARG cc_start: 0.8838 (ptm-80) cc_final: 0.8387 (mtm110) REVERT: c 81 TYR cc_start: 0.7175 (m-80) cc_final: 0.6690 (m-80) REVERT: c 82 PHE cc_start: 0.8160 (m-80) cc_final: 0.7952 (m-80) REVERT: c 84 ASN cc_start: 0.8135 (t0) cc_final: 0.6159 (t0) REVERT: c 86 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7548 (mt0) REVERT: c 110 MET cc_start: 0.8364 (mmm) cc_final: 0.7850 (mmm) REVERT: c 115 GLU cc_start: 0.7707 (tt0) cc_final: 0.7411 (tt0) REVERT: c 145 LEU cc_start: 0.8240 (mt) cc_final: 0.7980 (mt) REVERT: c 151 ARG cc_start: 0.8369 (ttm-80) cc_final: 0.7962 (ttm-80) REVERT: c 152 ASN cc_start: 0.8116 (t0) cc_final: 0.7496 (t0) REVERT: c 153 TRP cc_start: 0.8695 (p-90) cc_final: 0.8217 (p-90) REVERT: c 159 CYS cc_start: 0.8345 (t) cc_final: 0.8141 (t) REVERT: c 167 TYR cc_start: 0.8043 (m-10) cc_final: 0.7232 (m-10) REVERT: c 168 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7728 (mt-10) REVERT: c 171 ASP cc_start: 0.8356 (m-30) cc_final: 0.7975 (m-30) outliers start: 0 outliers final: 0 residues processed: 786 average time/residue: 0.1546 time to fit residues: 171.9371 Evaluate side-chains 762 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 762 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 103 optimal weight: 0.0270 chunk 188 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 86 optimal weight: 0.0770 chunk 34 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 72 optimal weight: 0.0060 chunk 179 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 159 optimal weight: 0.8980 overall best weight: 0.3212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 GLN M 36 GLN ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 321 GLN b 355 GLN ** m 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 36 GLN c 95 ASN ** c 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 411 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.140196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.115597 restraints weight = 30957.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.120026 restraints weight = 16703.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.122938 restraints weight = 10367.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.125076 restraints weight = 7122.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.126676 restraints weight = 5275.932| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16108 Z= 0.120 Angle : 0.556 7.458 21822 Z= 0.292 Chirality : 0.044 0.158 2524 Planarity : 0.004 0.042 2752 Dihedral : 9.890 169.419 2154 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.20), residues: 1954 helix: 1.28 (0.18), residues: 812 sheet: 0.29 (0.26), residues: 372 loop : 1.17 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 149 TYR 0.029 0.002 TYR M 110 PHE 0.024 0.001 PHE c 51 TRP 0.033 0.002 TRP c 172 HIS 0.007 0.001 HIS M 3 Details of bonding type rmsd covalent geometry : bond 0.00244 (16108) covalent geometry : angle 0.55604 (21822) hydrogen bonds : bond 0.04056 ( 815) hydrogen bonds : angle 5.03778 ( 2361) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 762 time to evaluate : 0.643 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: B 43 LYS cc_start: 0.8165 (mttt) cc_final: 0.7521 (mmmt) REVERT: B 47 LEU cc_start: 0.9008 (mt) cc_final: 0.8560 (mt) REVERT: B 50 MET cc_start: 0.8666 (mtm) cc_final: 0.8117 (mtm) REVERT: B 51 LEU cc_start: 0.8788 (mt) cc_final: 0.8444 (mt) REVERT: B 52 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7543 (mm-30) REVERT: B 63 MET cc_start: 0.8455 (mmm) cc_final: 0.7858 (mmm) REVERT: B 66 ILE cc_start: 0.8607 (mm) cc_final: 0.8295 (mm) REVERT: B 72 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8547 (mtpt) REVERT: B 74 LYS cc_start: 0.8781 (mmtt) cc_final: 0.8362 (mmtt) REVERT: B 80 PHE cc_start: 0.8365 (t80) cc_final: 0.7649 (t80) REVERT: B 83 VAL cc_start: 0.8367 (t) cc_final: 0.8103 (t) REVERT: B 84 VAL cc_start: 0.8592 (p) cc_final: 0.8241 (m) REVERT: B 85 LYS cc_start: 0.8595 (mttt) cc_final: 0.7968 (mttt) REVERT: B 90 LYS cc_start: 0.8339 (mttt) cc_final: 0.8068 (mttt) REVERT: B 94 ILE cc_start: 0.8212 (mt) cc_final: 0.8005 (mm) REVERT: B 98 VAL cc_start: 0.8597 (t) cc_final: 0.8382 (t) REVERT: B 101 TYR cc_start: 0.8416 (t80) cc_final: 0.8134 (t80) REVERT: B 112 LEU cc_start: 0.8162 (mt) cc_final: 0.7502 (mp) REVERT: B 125 LYS cc_start: 0.8866 (mttt) cc_final: 0.8368 (mtpp) REVERT: B 132 ARG cc_start: 0.8345 (mtt180) cc_final: 0.8088 (mtm180) REVERT: B 141 SER cc_start: 0.8527 (m) cc_final: 0.8300 (m) REVERT: B 147 ILE cc_start: 0.8337 (pt) cc_final: 0.7608 (pt) REVERT: B 151 MET cc_start: 0.7699 (mtp) cc_final: 0.6919 (mtp) REVERT: B 152 MET cc_start: 0.8072 (tpt) cc_final: 0.7794 (tpt) REVERT: B 155 ILE cc_start: 0.9187 (mm) cc_final: 0.8977 (mm) REVERT: B 167 ARG cc_start: 0.8467 (mtm-85) cc_final: 0.7659 (mtm-85) REVERT: B 169 ASN cc_start: 0.8668 (m-40) cc_final: 0.8417 (m-40) REVERT: B 175 GLN cc_start: 0.8515 (tm-30) cc_final: 0.7858 (tm-30) REVERT: B 181 ASP cc_start: 0.8254 (t0) cc_final: 0.7762 (t0) REVERT: B 190 GLU cc_start: 0.8204 (tt0) cc_final: 0.7948 (tt0) REVERT: B 193 GLU cc_start: 0.8419 (tt0) cc_final: 0.8149 (tt0) REVERT: B 196 LEU cc_start: 0.8863 (mt) cc_final: 0.8342 (tp) REVERT: B 202 LEU cc_start: 0.7304 (mm) cc_final: 0.6895 (tt) REVERT: B 207 VAL cc_start: 0.8814 (t) cc_final: 0.8460 (p) REVERT: B 213 GLU cc_start: 0.8156 (tt0) cc_final: 0.7679 (tt0) REVERT: B 228 LYS cc_start: 0.8577 (ttpt) cc_final: 0.8072 (ttpt) REVERT: B 244 ILE cc_start: 0.8960 (mt) cc_final: 0.8351 (tp) REVERT: B 246 HIS cc_start: 0.8449 (m-70) cc_final: 0.8123 (m-70) REVERT: B 247 MET cc_start: 0.7174 (tmm) cc_final: 0.6709 (tmm) REVERT: B 298 ARG cc_start: 0.8589 (mmm160) cc_final: 0.7865 (mpt180) REVERT: B 301 ILE cc_start: 0.8724 (mt) cc_final: 0.8427 (mt) REVERT: B 302 ARG cc_start: 0.8446 (ttm110) cc_final: 0.8196 (ttm-80) REVERT: B 305 LYS cc_start: 0.8679 (tttt) cc_final: 0.8463 (ttpp) REVERT: B 308 LEU cc_start: 0.8670 (mt) cc_final: 0.8335 (mm) REVERT: B 311 ARG cc_start: 0.8305 (ptt180) cc_final: 0.7533 (ptt-90) REVERT: B 317 MET cc_start: 0.8671 (tpp) cc_final: 0.8409 (tpp) REVERT: B 322 LEU cc_start: 0.8390 (tt) cc_final: 0.8164 (tt) REVERT: B 326 ILE cc_start: 0.8047 (mm) cc_final: 0.7707 (mm) REVERT: B 341 ARG cc_start: 0.8713 (ptt90) cc_final: 0.7925 (ttp80) REVERT: B 355 GLN cc_start: 0.8731 (mt0) cc_final: 0.8340 (mt0) REVERT: B 359 THR cc_start: 0.8057 (m) cc_final: 0.7765 (p) REVERT: B 387 THR cc_start: 0.8381 (m) cc_final: 0.8060 (m) REVERT: B 388 LEU cc_start: 0.8659 (mm) cc_final: 0.8449 (mm) REVERT: B 391 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7091 (mt-10) REVERT: B 417 ASP cc_start: 0.8137 (t0) cc_final: 0.7402 (m-30) REVERT: B 641 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7400 (pp20) REVERT: M 1 MET cc_start: 0.6973 (mpp) cc_final: 0.6611 (mpp) REVERT: M 17 GLU cc_start: 0.7497 (pt0) cc_final: 0.7025 (pt0) REVERT: M 29 CYS cc_start: 0.8621 (t) cc_final: 0.8206 (t) REVERT: M 34 GLU cc_start: 0.9040 (tt0) cc_final: 0.8832 (tt0) REVERT: M 43 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7446 (mt-10) REVERT: M 56 LEU cc_start: 0.8325 (mp) cc_final: 0.8087 (mm) REVERT: M 64 LEU cc_start: 0.8482 (tp) cc_final: 0.8244 (tp) REVERT: M 88 ASP cc_start: 0.8436 (m-30) cc_final: 0.8107 (m-30) REVERT: M 89 THR cc_start: 0.8974 (m) cc_final: 0.8627 (p) REVERT: M 92 ASP cc_start: 0.8053 (t0) cc_final: 0.7762 (t0) REVERT: M 116 MET cc_start: 0.7762 (mtm) cc_final: 0.7530 (mtm) REVERT: M 126 GLU cc_start: 0.8144 (tp30) cc_final: 0.7501 (tp30) REVERT: M 128 ASN cc_start: 0.8293 (m-40) cc_final: 0.7952 (m110) REVERT: M 131 LYS cc_start: 0.8481 (mtmm) cc_final: 0.7952 (mttp) REVERT: M 134 ILE cc_start: 0.8332 (mt) cc_final: 0.8027 (mt) REVERT: M 135 LYS cc_start: 0.8915 (mmtt) cc_final: 0.8371 (mmtt) REVERT: M 157 LEU cc_start: 0.8533 (mt) cc_final: 0.8258 (pp) REVERT: M 159 THR cc_start: 0.8143 (m) cc_final: 0.7910 (p) REVERT: M 161 GLN cc_start: 0.8309 (tp40) cc_final: 0.7993 (tp-100) REVERT: M 173 LYS cc_start: 0.7915 (tttt) cc_final: 0.7620 (tttt) REVERT: M 174 TYR cc_start: 0.7571 (m-80) cc_final: 0.7134 (m-80) REVERT: M 203 GLN cc_start: 0.7106 (mm-40) cc_final: 0.6823 (mm-40) REVERT: M 209 CYS cc_start: 0.7505 (t) cc_final: 0.6624 (m) REVERT: M 220 LEU cc_start: 0.8049 (mm) cc_final: 0.7633 (mm) REVERT: M 227 LEU cc_start: 0.8894 (mt) cc_final: 0.8575 (mp) REVERT: M 234 HIS cc_start: 0.7910 (t-90) cc_final: 0.7651 (t-90) REVERT: M 240 LYS cc_start: 0.8448 (mttt) cc_final: 0.7934 (mttt) REVERT: M 242 TRP cc_start: 0.7517 (t-100) cc_final: 0.7118 (t-100) REVERT: M 245 GLU cc_start: 0.6871 (mm-30) cc_final: 0.6320 (mm-30) REVERT: M 257 PHE cc_start: 0.8447 (p90) cc_final: 0.8104 (p90) REVERT: M 258 ARG cc_start: 0.8403 (mtm-85) cc_final: 0.7915 (mtm180) REVERT: M 262 TYR cc_start: 0.8398 (p90) cc_final: 0.8020 (p90) REVERT: M 298 LYS cc_start: 0.8996 (tttt) cc_final: 0.8604 (tttt) REVERT: M 300 ASN cc_start: 0.9008 (p0) cc_final: 0.8774 (p0) REVERT: M 393 ASP cc_start: 0.7976 (t0) cc_final: 0.7516 (t0) REVERT: M 402 PHE cc_start: 0.7734 (m-80) cc_final: 0.7158 (m-80) REVERT: M 414 PHE cc_start: 0.7807 (t80) cc_final: 0.7363 (t80) REVERT: C 18 MET cc_start: 0.6467 (mmm) cc_final: 0.6176 (mmm) REVERT: C 31 THR cc_start: 0.8087 (p) cc_final: 0.7863 (p) REVERT: C 44 THR cc_start: 0.9140 (m) cc_final: 0.8771 (p) REVERT: C 57 GLU cc_start: 0.7831 (tt0) cc_final: 0.7615 (tt0) REVERT: C 64 THR cc_start: 0.6615 (m) cc_final: 0.6319 (t) REVERT: C 78 TRP cc_start: 0.8192 (m-10) cc_final: 0.7628 (m-10) REVERT: C 82 PHE cc_start: 0.7860 (m-10) cc_final: 0.7506 (m-80) REVERT: C 84 ASN cc_start: 0.8486 (t0) cc_final: 0.7843 (t0) REVERT: C 86 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7193 (mt0) REVERT: C 110 MET cc_start: 0.8348 (mmm) cc_final: 0.7970 (mmm) REVERT: C 115 GLU cc_start: 0.8220 (tt0) cc_final: 0.7833 (tt0) REVERT: C 142 LYS cc_start: 0.8938 (mttm) cc_final: 0.8626 (mttm) REVERT: C 145 LEU cc_start: 0.8059 (mt) cc_final: 0.7779 (mt) REVERT: C 153 TRP cc_start: 0.8470 (p-90) cc_final: 0.8270 (p-90) REVERT: C 168 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7575 (mt-10) REVERT: C 171 ASP cc_start: 0.8072 (m-30) cc_final: 0.7782 (m-30) REVERT: C 172 TRP cc_start: 0.8225 (t60) cc_final: 0.7906 (t60) REVERT: C 178 ARG cc_start: 0.7792 (ttm170) cc_final: 0.7589 (ttm170) REVERT: b 43 LYS cc_start: 0.8120 (mttt) cc_final: 0.7698 (tttp) REVERT: b 47 LEU cc_start: 0.8922 (mt) cc_final: 0.8554 (mt) REVERT: b 50 MET cc_start: 0.8481 (mtm) cc_final: 0.8211 (mtm) REVERT: b 51 LEU cc_start: 0.8803 (mt) cc_final: 0.8416 (mt) REVERT: b 54 ASN cc_start: 0.7642 (m110) cc_final: 0.7357 (m110) REVERT: b 59 LYS cc_start: 0.8593 (mtmm) cc_final: 0.8310 (mttp) REVERT: b 63 MET cc_start: 0.8441 (mmm) cc_final: 0.7859 (mmm) REVERT: b 66 ILE cc_start: 0.8420 (mm) cc_final: 0.8097 (mm) REVERT: b 72 LYS cc_start: 0.8776 (mmtt) cc_final: 0.8234 (mtpt) REVERT: b 80 PHE cc_start: 0.8391 (t80) cc_final: 0.7738 (t80) REVERT: b 85 LYS cc_start: 0.8566 (mttt) cc_final: 0.8195 (mttt) REVERT: b 98 VAL cc_start: 0.8815 (t) cc_final: 0.8560 (t) REVERT: b 112 LEU cc_start: 0.8024 (mp) cc_final: 0.6986 (mp) REVERT: b 132 ARG cc_start: 0.8367 (mtt180) cc_final: 0.8115 (mtm180) REVERT: b 141 SER cc_start: 0.8469 (m) cc_final: 0.8266 (m) REVERT: b 150 ILE cc_start: 0.8195 (mt) cc_final: 0.7943 (mt) REVERT: b 151 MET cc_start: 0.7532 (mtp) cc_final: 0.7069 (mtp) REVERT: b 155 ILE cc_start: 0.9215 (mm) cc_final: 0.9013 (mm) REVERT: b 162 LEU cc_start: 0.7808 (mp) cc_final: 0.6989 (tp) REVERT: b 186 GLU cc_start: 0.8292 (pm20) cc_final: 0.7927 (pm20) REVERT: b 187 MET cc_start: 0.8286 (mtm) cc_final: 0.7630 (mtm) REVERT: b 193 GLU cc_start: 0.8440 (tt0) cc_final: 0.8107 (tt0) REVERT: b 195 LEU cc_start: 0.9057 (mt) cc_final: 0.8701 (mt) REVERT: b 202 LEU cc_start: 0.7411 (mm) cc_final: 0.6977 (tp) REVERT: b 207 VAL cc_start: 0.8847 (t) cc_final: 0.8377 (p) REVERT: b 209 MET cc_start: 0.7423 (tmm) cc_final: 0.7180 (tmm) REVERT: b 212 GLU cc_start: 0.7985 (tp30) cc_final: 0.7670 (tp30) REVERT: b 228 LYS cc_start: 0.8572 (ttpt) cc_final: 0.8161 (ttpt) REVERT: b 244 ILE cc_start: 0.9042 (mt) cc_final: 0.8640 (tp) REVERT: b 247 MET cc_start: 0.7166 (tmm) cc_final: 0.6519 (tmm) REVERT: b 298 ARG cc_start: 0.8839 (mmm160) cc_final: 0.7394 (mpt180) REVERT: b 307 LEU cc_start: 0.8890 (mt) cc_final: 0.8515 (mt) REVERT: b 308 LEU cc_start: 0.8745 (mt) cc_final: 0.8468 (mm) REVERT: b 311 ARG cc_start: 0.8338 (ptt180) cc_final: 0.7782 (ptt-90) REVERT: b 317 MET cc_start: 0.8689 (tpp) cc_final: 0.8352 (tpp) REVERT: b 321 GLN cc_start: 0.7915 (tt0) cc_final: 0.7404 (tt0) REVERT: b 322 LEU cc_start: 0.8437 (tt) cc_final: 0.8209 (tt) REVERT: b 324 TRP cc_start: 0.8677 (t-100) cc_final: 0.7835 (t-100) REVERT: b 326 ILE cc_start: 0.8017 (mm) cc_final: 0.7755 (mm) REVERT: b 331 GLU cc_start: 0.7187 (mp0) cc_final: 0.6781 (mp0) REVERT: b 341 ARG cc_start: 0.8666 (ptt90) cc_final: 0.7976 (ttp80) REVERT: b 346 ASN cc_start: 0.7151 (p0) cc_final: 0.6576 (p0) REVERT: b 360 MET cc_start: 0.8351 (ttm) cc_final: 0.6138 (ttm) REVERT: b 384 MET cc_start: 0.7864 (ptt) cc_final: 0.7346 (ptt) REVERT: b 627 ASN cc_start: 0.8583 (m110) cc_final: 0.8370 (m-40) REVERT: m 1 MET cc_start: 0.6914 (mtt) cc_final: 0.6454 (mtt) REVERT: m 17 GLU cc_start: 0.7475 (pt0) cc_final: 0.7197 (pt0) REVERT: m 21 LYS cc_start: 0.7760 (mttt) cc_final: 0.7141 (mttm) REVERT: m 29 CYS cc_start: 0.8365 (m) cc_final: 0.7799 (t) REVERT: m 36 GLN cc_start: 0.8417 (tp-100) cc_final: 0.8007 (tp-100) REVERT: m 37 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8411 (tm-30) REVERT: m 43 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7544 (mt-10) REVERT: m 44 ASN cc_start: 0.8208 (t0) cc_final: 0.7485 (t0) REVERT: m 45 VAL cc_start: 0.8843 (t) cc_final: 0.8569 (t) REVERT: m 77 LEU cc_start: 0.8508 (mt) cc_final: 0.8249 (mt) REVERT: m 78 PHE cc_start: 0.8753 (t80) cc_final: 0.8330 (t80) REVERT: m 80 ILE cc_start: 0.8509 (mt) cc_final: 0.8203 (mm) REVERT: m 88 ASP cc_start: 0.8328 (m-30) cc_final: 0.8126 (m-30) REVERT: m 89 THR cc_start: 0.8827 (m) cc_final: 0.8537 (p) REVERT: m 108 ILE cc_start: 0.8830 (mt) cc_final: 0.8565 (mm) REVERT: m 111 GLU cc_start: 0.8065 (tt0) cc_final: 0.7739 (tt0) REVERT: m 116 MET cc_start: 0.7585 (mtm) cc_final: 0.7202 (mtm) REVERT: m 119 ASN cc_start: 0.8258 (t0) cc_final: 0.7649 (t0) REVERT: m 128 ASN cc_start: 0.8242 (m-40) cc_final: 0.8037 (m-40) REVERT: m 131 LYS cc_start: 0.8539 (mtmm) cc_final: 0.8308 (mttp) REVERT: m 134 ILE cc_start: 0.8050 (mt) cc_final: 0.7710 (tp) REVERT: m 140 LEU cc_start: 0.8450 (mt) cc_final: 0.8212 (tt) REVERT: m 141 ARG cc_start: 0.8117 (mmt90) cc_final: 0.7746 (mmt90) REVERT: m 209 CYS cc_start: 0.7252 (t) cc_final: 0.6265 (m) REVERT: m 234 HIS cc_start: 0.8011 (t-90) cc_final: 0.7810 (t-90) REVERT: m 239 PHE cc_start: 0.7867 (p90) cc_final: 0.7663 (p90) REVERT: m 240 LYS cc_start: 0.8619 (mttt) cc_final: 0.7850 (mmmm) REVERT: m 243 GLU cc_start: 0.8518 (tp30) cc_final: 0.8099 (tp30) REVERT: m 250 PHE cc_start: 0.6766 (p90) cc_final: 0.6447 (p90) REVERT: m 257 PHE cc_start: 0.8549 (p90) cc_final: 0.8295 (p90) REVERT: m 258 ARG cc_start: 0.8538 (mtp-110) cc_final: 0.8280 (mtm110) REVERT: m 262 TYR cc_start: 0.8152 (p90) cc_final: 0.7054 (p90) REVERT: m 272 ILE cc_start: 0.7743 (mm) cc_final: 0.6792 (mm) REVERT: m 293 ILE cc_start: 0.7800 (mm) cc_final: 0.7386 (pt) REVERT: m 298 LYS cc_start: 0.9064 (tttt) cc_final: 0.8679 (tttt) REVERT: m 300 ASN cc_start: 0.8997 (p0) cc_final: 0.8782 (p0) REVERT: m 373 LEU cc_start: 0.7465 (tt) cc_final: 0.7231 (tt) REVERT: m 393 ASP cc_start: 0.8066 (t0) cc_final: 0.7600 (t0) REVERT: m 402 PHE cc_start: 0.7656 (m-80) cc_final: 0.7222 (m-80) REVERT: m 406 LYS cc_start: 0.8602 (ttmt) cc_final: 0.8255 (ttmt) REVERT: m 407 TYR cc_start: 0.8288 (m-10) cc_final: 0.8060 (m-80) REVERT: m 414 PHE cc_start: 0.7917 (t80) cc_final: 0.7467 (t80) REVERT: c 19 ARG cc_start: 0.7105 (ttm170) cc_final: 0.5866 (ttm170) REVERT: c 30 LYS cc_start: 0.8506 (mttp) cc_final: 0.8192 (mttp) REVERT: c 53 VAL cc_start: 0.8355 (p) cc_final: 0.8107 (m) REVERT: c 58 TYR cc_start: 0.8073 (t80) cc_final: 0.7600 (t80) REVERT: c 64 THR cc_start: 0.6694 (m) cc_final: 0.6306 (t) REVERT: c 68 VAL cc_start: 0.8031 (t) cc_final: 0.7731 (p) REVERT: c 78 TRP cc_start: 0.8199 (m-10) cc_final: 0.7406 (m-10) REVERT: c 79 ARG cc_start: 0.8786 (ptm-80) cc_final: 0.8287 (mtm110) REVERT: c 81 TYR cc_start: 0.7250 (m-80) cc_final: 0.6901 (m-80) REVERT: c 82 PHE cc_start: 0.8049 (m-10) cc_final: 0.7776 (m-80) REVERT: c 84 ASN cc_start: 0.8236 (t0) cc_final: 0.6230 (t0) REVERT: c 110 MET cc_start: 0.8357 (mmm) cc_final: 0.7831 (mmm) REVERT: c 115 GLU cc_start: 0.7678 (tt0) cc_final: 0.7347 (tt0) REVERT: c 145 LEU cc_start: 0.8214 (mt) cc_final: 0.7942 (mt) REVERT: c 152 ASN cc_start: 0.7949 (t0) cc_final: 0.7628 (t0) REVERT: c 153 TRP cc_start: 0.8663 (p-90) cc_final: 0.8186 (p-90) REVERT: c 159 CYS cc_start: 0.8294 (t) cc_final: 0.8047 (t) REVERT: c 167 TYR cc_start: 0.8020 (m-10) cc_final: 0.7174 (m-10) REVERT: c 168 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7706 (mt-10) REVERT: c 171 ASP cc_start: 0.8212 (m-30) cc_final: 0.7873 (m-30) REVERT: c 172 TRP cc_start: 0.8345 (t60) cc_final: 0.6956 (t60) REVERT: c 176 GLN cc_start: 0.8472 (pt0) cc_final: 0.8131 (pt0) REVERT: c 178 ARG cc_start: 0.7846 (ttm170) cc_final: 0.7626 (ttm170) REVERT: y 410 SER cc_start: 0.7595 (m) cc_final: 0.7127 (p) outliers start: 0 outliers final: 0 residues processed: 762 average time/residue: 0.1534 time to fit residues: 165.7836 Evaluate side-chains 742 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 742 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 15 optimal weight: 0.0070 chunk 143 optimal weight: 1.9990 chunk 91 optimal weight: 0.0030 chunk 54 optimal weight: 0.9990 chunk 107 optimal weight: 0.2980 chunk 69 optimal weight: 8.9990 chunk 2 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 overall best weight: 0.3608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 GLN ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN c 95 ASN ** c 176 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 = 0.3830 r_free = 0.3830 target = 0.140086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.115687 restraints weight = 30690.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.120050 restraints weight = 16535.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.123093 restraints weight = 10321.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.124955 restraints weight = 7038.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.126572 restraints weight = 5274.596| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16108 Z= 0.120 Angle : 0.553 7.830 21822 Z= 0.289 Chirality : 0.044 0.234 2524 Planarity : 0.004 0.068 2752 Dihedral : 9.623 168.405 2154 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.20), residues: 1954 helix: 1.30 (0.18), residues: 808 sheet: 0.36 (0.27), residues: 380 loop : 1.24 (0.25), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 218 TYR 0.020 0.002 TYR C 167 PHE 0.027 0.001 PHE m 121 TRP 0.027 0.002 TRP c 172 HIS 0.004 0.001 HIS M 3 Details of bonding type rmsd covalent geometry : bond 0.00243 (16108) covalent geometry : angle 0.55299 (21822) hydrogen bonds : bond 0.03979 ( 815) hydrogen bonds : angle 4.91094 ( 2361) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 762 time to evaluate : 0.621 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: B 43 LYS cc_start: 0.8151 (mttt) cc_final: 0.7511 (mmmt) REVERT: B 47 LEU cc_start: 0.9038 (mt) cc_final: 0.8612 (mt) REVERT: B 50 MET cc_start: 0.8624 (mtm) cc_final: 0.8127 (mtm) REVERT: B 51 LEU cc_start: 0.8814 (mt) cc_final: 0.8479 (mt) REVERT: B 52 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7603 (mm-30) REVERT: B 54 ASN cc_start: 0.7868 (m110) cc_final: 0.7473 (m110) REVERT: B 55 LYS cc_start: 0.8286 (mtpt) cc_final: 0.7846 (mtpt) REVERT: B 59 LYS cc_start: 0.8677 (mtmm) cc_final: 0.8271 (ptpp) REVERT: B 63 MET cc_start: 0.8476 (mmm) cc_final: 0.7848 (mmm) REVERT: B 66 ILE cc_start: 0.8593 (mm) cc_final: 0.8344 (mm) REVERT: B 72 LYS cc_start: 0.8838 (mmtt) cc_final: 0.8562 (mtpt) REVERT: B 74 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8272 (mmtt) REVERT: B 79 LEU cc_start: 0.8514 (mt) cc_final: 0.8282 (mt) REVERT: B 80 PHE cc_start: 0.8479 (t80) cc_final: 0.7836 (t80) REVERT: B 83 VAL cc_start: 0.8308 (t) cc_final: 0.8102 (t) REVERT: B 85 LYS cc_start: 0.8569 (mttt) cc_final: 0.7825 (mttt) REVERT: B 90 LYS cc_start: 0.8411 (mttt) cc_final: 0.8107 (mttt) REVERT: B 107 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7390 (mt-10) REVERT: B 112 LEU cc_start: 0.8122 (mt) cc_final: 0.7478 (mp) REVERT: B 125 LYS cc_start: 0.8806 (mttt) cc_final: 0.8416 (mtpp) REVERT: B 132 ARG cc_start: 0.8296 (mtt180) cc_final: 0.8028 (mtm180) REVERT: B 147 ILE cc_start: 0.8358 (pt) cc_final: 0.7569 (pt) REVERT: B 151 MET cc_start: 0.7699 (mtp) cc_final: 0.6840 (mtp) REVERT: B 155 ILE cc_start: 0.9190 (mm) cc_final: 0.8926 (mm) REVERT: B 169 ASN cc_start: 0.8647 (m-40) cc_final: 0.8358 (m-40) REVERT: B 175 GLN cc_start: 0.8541 (tm-30) cc_final: 0.7897 (tm-30) REVERT: B 177 LEU cc_start: 0.8462 (tp) cc_final: 0.8221 (tp) REVERT: B 181 ASP cc_start: 0.8309 (t0) cc_final: 0.7842 (t0) REVERT: B 185 LYS cc_start: 0.8478 (ptmm) cc_final: 0.8180 (ptmm) REVERT: B 190 GLU cc_start: 0.8114 (tt0) cc_final: 0.7868 (tt0) REVERT: B 193 GLU cc_start: 0.8419 (tt0) cc_final: 0.8182 (tt0) REVERT: B 196 LEU cc_start: 0.8869 (mt) cc_final: 0.8191 (tt) REVERT: B 202 LEU cc_start: 0.7237 (mm) cc_final: 0.6892 (tt) REVERT: B 207 VAL cc_start: 0.8804 (t) cc_final: 0.8430 (p) REVERT: B 213 GLU cc_start: 0.8167 (tt0) cc_final: 0.7705 (tt0) REVERT: B 215 CYS cc_start: 0.8623 (m) cc_final: 0.8404 (p) REVERT: B 228 LYS cc_start: 0.8609 (ttpt) cc_final: 0.8091 (ttpt) REVERT: B 241 GLN cc_start: 0.8239 (mt0) cc_final: 0.7410 (mt0) REVERT: B 244 ILE cc_start: 0.8961 (mt) cc_final: 0.8458 (tp) REVERT: B 247 MET cc_start: 0.7131 (tmm) cc_final: 0.6639 (tmm) REVERT: B 298 ARG cc_start: 0.8639 (mmm160) cc_final: 0.7852 (mpt180) REVERT: B 305 LYS cc_start: 0.8701 (tttt) cc_final: 0.8410 (tttm) REVERT: B 308 LEU cc_start: 0.8624 (mt) cc_final: 0.8316 (mm) REVERT: B 311 ARG cc_start: 0.8255 (ptt180) cc_final: 0.7565 (ptt-90) REVERT: B 317 MET cc_start: 0.8651 (tpp) cc_final: 0.8316 (tpp) REVERT: B 321 GLN cc_start: 0.7998 (tt0) cc_final: 0.7552 (tt0) REVERT: B 326 ILE cc_start: 0.8030 (mm) cc_final: 0.7752 (mm) REVERT: B 341 ARG cc_start: 0.8661 (ptt90) cc_final: 0.8187 (ptm-80) REVERT: B 387 THR cc_start: 0.8378 (m) cc_final: 0.8047 (m) REVERT: B 388 LEU cc_start: 0.8711 (mm) cc_final: 0.8466 (mm) REVERT: B 391 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7020 (mt-10) REVERT: B 417 ASP cc_start: 0.8039 (t0) cc_final: 0.7509 (m-30) REVERT: M 17 GLU cc_start: 0.7446 (pt0) cc_final: 0.7077 (pt0) REVERT: M 29 CYS cc_start: 0.8597 (t) cc_final: 0.8161 (t) REVERT: M 30 ASP cc_start: 0.7878 (t0) cc_final: 0.7664 (t0) REVERT: M 34 GLU cc_start: 0.9031 (tt0) cc_final: 0.8827 (tt0) REVERT: M 43 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7516 (mt-10) REVERT: M 64 LEU cc_start: 0.8515 (tp) cc_final: 0.8283 (tp) REVERT: M 77 LEU cc_start: 0.8395 (mt) cc_final: 0.7942 (mt) REVERT: M 78 PHE cc_start: 0.8706 (t80) cc_final: 0.8456 (t80) REVERT: M 88 ASP cc_start: 0.8396 (m-30) cc_final: 0.8071 (m-30) REVERT: M 89 THR cc_start: 0.9027 (m) cc_final: 0.8723 (p) REVERT: M 92 ASP cc_start: 0.8030 (t0) cc_final: 0.7807 (t0) REVERT: M 116 MET cc_start: 0.7824 (mtm) cc_final: 0.7505 (mtm) REVERT: M 123 LEU cc_start: 0.8552 (tp) cc_final: 0.8314 (tp) REVERT: M 126 GLU cc_start: 0.8073 (tp30) cc_final: 0.7462 (tp30) REVERT: M 128 ASN cc_start: 0.8263 (m-40) cc_final: 0.7906 (m-40) REVERT: M 131 LYS cc_start: 0.8498 (mtmm) cc_final: 0.7902 (mttp) REVERT: M 134 ILE cc_start: 0.8314 (mt) cc_final: 0.7802 (mt) REVERT: M 135 LYS cc_start: 0.8914 (mmtt) cc_final: 0.8322 (mmtt) REVERT: M 157 LEU cc_start: 0.8470 (mt) cc_final: 0.8215 (pp) REVERT: M 173 LYS cc_start: 0.8041 (tttt) cc_final: 0.7719 (tttt) REVERT: M 174 TYR cc_start: 0.7637 (m-80) cc_final: 0.7181 (m-80) REVERT: M 209 CYS cc_start: 0.7449 (t) cc_final: 0.6635 (m) REVERT: M 220 LEU cc_start: 0.8034 (mm) cc_final: 0.7651 (mm) REVERT: M 227 LEU cc_start: 0.8894 (mt) cc_final: 0.8575 (mp) REVERT: M 234 HIS cc_start: 0.7987 (t-90) cc_final: 0.7667 (t-90) REVERT: M 242 TRP cc_start: 0.7600 (t-100) cc_final: 0.7052 (t-100) REVERT: M 245 GLU cc_start: 0.6727 (mm-30) cc_final: 0.6146 (mm-30) REVERT: M 257 PHE cc_start: 0.8454 (p90) cc_final: 0.8108 (p90) REVERT: M 262 TYR cc_start: 0.8387 (p90) cc_final: 0.8114 (p90) REVERT: M 298 LYS cc_start: 0.8993 (tttt) cc_final: 0.8581 (tttt) REVERT: M 300 ASN cc_start: 0.8998 (p0) cc_final: 0.8689 (p0) REVERT: M 393 ASP cc_start: 0.7914 (t0) cc_final: 0.7471 (t0) REVERT: M 402 PHE cc_start: 0.7702 (m-80) cc_final: 0.7153 (m-80) REVERT: M 414 PHE cc_start: 0.7852 (t80) cc_final: 0.7386 (t80) REVERT: C 18 MET cc_start: 0.6365 (mmm) cc_final: 0.6033 (mmm) REVERT: C 44 THR cc_start: 0.9131 (m) cc_final: 0.8763 (p) REVERT: C 64 THR cc_start: 0.6632 (m) cc_final: 0.6354 (t) REVERT: C 78 TRP cc_start: 0.8221 (m-10) cc_final: 0.7660 (m-10) REVERT: C 81 TYR cc_start: 0.7227 (m-80) cc_final: 0.6532 (m-80) REVERT: C 82 PHE cc_start: 0.7825 (m-10) cc_final: 0.7459 (m-80) REVERT: C 84 ASN cc_start: 0.8458 (t0) cc_final: 0.7709 (t0) REVERT: C 86 GLN cc_start: 0.7885 (mm-40) cc_final: 0.7229 (mt0) REVERT: C 110 MET cc_start: 0.8339 (mmm) cc_final: 0.7938 (mmm) REVERT: C 115 GLU cc_start: 0.8160 (tt0) cc_final: 0.7774 (tt0) REVERT: C 142 LYS cc_start: 0.8929 (mttm) cc_final: 0.8667 (mttm) REVERT: C 145 LEU cc_start: 0.7976 (mt) cc_final: 0.7657 (mt) REVERT: C 153 TRP cc_start: 0.8481 (p-90) cc_final: 0.7872 (p-90) REVERT: C 168 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7569 (mt-10) REVERT: C 171 ASP cc_start: 0.8031 (m-30) cc_final: 0.7695 (m-30) REVERT: C 172 TRP cc_start: 0.8230 (t60) cc_final: 0.7658 (t60) REVERT: C 178 ARG cc_start: 0.7886 (ttm170) cc_final: 0.7614 (ttm170) REVERT: b 43 LYS cc_start: 0.8096 (mttt) cc_final: 0.7678 (tttp) REVERT: b 45 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7255 (mm-30) REVERT: b 47 LEU cc_start: 0.8915 (mt) cc_final: 0.8525 (mt) REVERT: b 50 MET cc_start: 0.8451 (mtm) cc_final: 0.8183 (mtm) REVERT: b 51 LEU cc_start: 0.8907 (mt) cc_final: 0.8571 (mt) REVERT: b 66 ILE cc_start: 0.8327 (mm) cc_final: 0.7945 (mm) REVERT: b 72 LYS cc_start: 0.8711 (mmtt) cc_final: 0.8210 (mtmt) REVERT: b 80 PHE cc_start: 0.8407 (t80) cc_final: 0.7752 (t80) REVERT: b 90 LYS cc_start: 0.8122 (mttm) cc_final: 0.7920 (mmmm) REVERT: b 101 TYR cc_start: 0.8776 (t80) cc_final: 0.8463 (t80) REVERT: b 102 LEU cc_start: 0.8987 (mt) cc_final: 0.8781 (mt) REVERT: b 112 LEU cc_start: 0.8045 (mp) cc_final: 0.6970 (mp) REVERT: b 121 GLN cc_start: 0.8075 (tt0) cc_final: 0.7731 (mt0) REVERT: b 132 ARG cc_start: 0.8341 (mtt180) cc_final: 0.8066 (mtm180) REVERT: b 147 ILE cc_start: 0.8383 (pt) cc_final: 0.7573 (pt) REVERT: b 150 ILE cc_start: 0.8212 (mt) cc_final: 0.7685 (mt) REVERT: b 151 MET cc_start: 0.7493 (mtp) cc_final: 0.6785 (mtp) REVERT: b 152 MET cc_start: 0.8028 (tpt) cc_final: 0.7804 (tpt) REVERT: b 162 LEU cc_start: 0.7946 (mp) cc_final: 0.7136 (tp) REVERT: b 186 GLU cc_start: 0.8317 (pm20) cc_final: 0.8063 (pm20) REVERT: b 187 MET cc_start: 0.8310 (mtm) cc_final: 0.7732 (mtm) REVERT: b 193 GLU cc_start: 0.8506 (tt0) cc_final: 0.8010 (tt0) REVERT: b 195 LEU cc_start: 0.9071 (mt) cc_final: 0.8721 (mt) REVERT: b 202 LEU cc_start: 0.7397 (mm) cc_final: 0.6961 (tp) REVERT: b 207 VAL cc_start: 0.8829 (t) cc_final: 0.8444 (p) REVERT: b 218 ARG cc_start: 0.9039 (mmm160) cc_final: 0.8600 (mtp85) REVERT: b 221 LEU cc_start: 0.9156 (mt) cc_final: 0.8885 (mt) REVERT: b 228 LYS cc_start: 0.8564 (ttpt) cc_final: 0.8126 (ttpt) REVERT: b 237 GLU cc_start: 0.7641 (tt0) cc_final: 0.7304 (tt0) REVERT: b 241 GLN cc_start: 0.8104 (mt0) cc_final: 0.7537 (mt0) REVERT: b 244 ILE cc_start: 0.9050 (mt) cc_final: 0.8632 (tp) REVERT: b 247 MET cc_start: 0.7201 (tmm) cc_final: 0.6539 (tmm) REVERT: b 298 ARG cc_start: 0.8871 (mmm160) cc_final: 0.7408 (mpt180) REVERT: b 307 LEU cc_start: 0.8887 (mt) cc_final: 0.8539 (mt) REVERT: b 308 LEU cc_start: 0.8810 (mt) cc_final: 0.8454 (mm) REVERT: b 311 ARG cc_start: 0.8318 (ptt180) cc_final: 0.7690 (ptt-90) REVERT: b 321 GLN cc_start: 0.7941 (tt0) cc_final: 0.7477 (tt0) REVERT: b 322 LEU cc_start: 0.8476 (tt) cc_final: 0.8194 (tt) REVERT: b 326 ILE cc_start: 0.7974 (mm) cc_final: 0.7705 (mm) REVERT: b 331 GLU cc_start: 0.7133 (mp0) cc_final: 0.6787 (mp0) REVERT: b 341 ARG cc_start: 0.8660 (ptt90) cc_final: 0.8003 (ptm-80) REVERT: b 346 ASN cc_start: 0.7168 (p0) cc_final: 0.6641 (p0) REVERT: b 360 MET cc_start: 0.8315 (ttm) cc_final: 0.7920 (ttm) REVERT: b 384 MET cc_start: 0.7839 (ptt) cc_final: 0.7368 (ptt) REVERT: b 627 ASN cc_start: 0.8626 (m110) cc_final: 0.8373 (m110) REVERT: m 1 MET cc_start: 0.6937 (mtt) cc_final: 0.6496 (mtt) REVERT: m 14 ILE cc_start: 0.8156 (tt) cc_final: 0.7870 (mt) REVERT: m 17 GLU cc_start: 0.7480 (pt0) cc_final: 0.7190 (pt0) REVERT: m 21 LYS cc_start: 0.7816 (mttt) cc_final: 0.7328 (mttp) REVERT: m 29 CYS cc_start: 0.8451 (m) cc_final: 0.7892 (t) REVERT: m 36 GLN cc_start: 0.8400 (tp-100) cc_final: 0.8007 (tp-100) REVERT: m 37 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8432 (tm-30) REVERT: m 43 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7590 (mt-10) REVERT: m 44 ASN cc_start: 0.8182 (t0) cc_final: 0.7460 (t0) REVERT: m 45 VAL cc_start: 0.8858 (t) cc_final: 0.8646 (t) REVERT: m 71 GLN cc_start: 0.8342 (tp40) cc_final: 0.7927 (tp-100) REVERT: m 77 LEU cc_start: 0.8537 (mt) cc_final: 0.8299 (mt) REVERT: m 78 PHE cc_start: 0.8763 (t80) cc_final: 0.8418 (t80) REVERT: m 80 ILE cc_start: 0.8522 (mt) cc_final: 0.8233 (mm) REVERT: m 89 THR cc_start: 0.8906 (m) cc_final: 0.8576 (p) REVERT: m 90 PHE cc_start: 0.8691 (m-10) cc_final: 0.8415 (m-10) REVERT: m 94 PHE cc_start: 0.6880 (m-10) cc_final: 0.6675 (m-10) REVERT: m 108 ILE cc_start: 0.8801 (mt) cc_final: 0.8542 (mm) REVERT: m 111 GLU cc_start: 0.8076 (tt0) cc_final: 0.7725 (tt0) REVERT: m 116 MET cc_start: 0.7492 (mtm) cc_final: 0.7291 (mtm) REVERT: m 123 LEU cc_start: 0.8490 (tp) cc_final: 0.8248 (tp) REVERT: m 131 LYS cc_start: 0.8548 (mtmm) cc_final: 0.8023 (mttp) REVERT: m 134 ILE cc_start: 0.8240 (mt) cc_final: 0.7721 (tp) REVERT: m 140 LEU cc_start: 0.8431 (mt) cc_final: 0.8211 (tt) REVERT: m 141 ARG cc_start: 0.8134 (mmt90) cc_final: 0.7714 (mmt90) REVERT: m 209 CYS cc_start: 0.7374 (t) cc_final: 0.6446 (m) REVERT: m 220 LEU cc_start: 0.7688 (mm) cc_final: 0.7387 (mm) REVERT: m 234 HIS cc_start: 0.7996 (t-90) cc_final: 0.7690 (t-90) REVERT: m 240 LYS cc_start: 0.8625 (mttt) cc_final: 0.7815 (mmmm) REVERT: m 243 GLU cc_start: 0.8519 (tp30) cc_final: 0.8126 (tp30) REVERT: m 257 PHE cc_start: 0.8538 (p90) cc_final: 0.8289 (p90) REVERT: m 258 ARG cc_start: 0.8569 (mtp-110) cc_final: 0.8339 (mtm110) REVERT: m 262 TYR cc_start: 0.8163 (p90) cc_final: 0.7018 (p90) REVERT: m 298 LYS cc_start: 0.9051 (tttt) cc_final: 0.8661 (tttt) REVERT: m 300 ASN cc_start: 0.8985 (p0) cc_final: 0.8690 (p0) REVERT: m 393 ASP cc_start: 0.7981 (t0) cc_final: 0.7478 (t0) REVERT: m 402 PHE cc_start: 0.7800 (m-80) cc_final: 0.7265 (m-80) REVERT: m 406 LYS cc_start: 0.8607 (ttmt) cc_final: 0.8270 (ttmt) REVERT: m 414 PHE cc_start: 0.7939 (t80) cc_final: 0.7470 (t80) REVERT: c 30 LYS cc_start: 0.8451 (mttp) cc_final: 0.8113 (mttp) REVERT: c 44 THR cc_start: 0.9212 (m) cc_final: 0.8828 (p) REVERT: c 45 THR cc_start: 0.8887 (p) cc_final: 0.8653 (p) REVERT: c 58 TYR cc_start: 0.8172 (t80) cc_final: 0.7194 (t80) REVERT: c 64 THR cc_start: 0.6734 (m) cc_final: 0.6303 (t) REVERT: c 68 VAL cc_start: 0.8010 (t) cc_final: 0.7712 (p) REVERT: c 78 TRP cc_start: 0.8235 (m-10) cc_final: 0.7467 (m-10) REVERT: c 79 ARG cc_start: 0.8816 (ptm-80) cc_final: 0.8292 (mtm110) REVERT: c 82 PHE cc_start: 0.8063 (m-10) cc_final: 0.7752 (m-80) REVERT: c 84 ASN cc_start: 0.8291 (t0) cc_final: 0.7316 (t0) REVERT: c 110 MET cc_start: 0.8321 (mmm) cc_final: 0.7838 (mmm) REVERT: c 115 GLU cc_start: 0.7717 (tt0) cc_final: 0.7343 (tt0) REVERT: c 135 ASN cc_start: 0.8130 (p0) cc_final: 0.7749 (p0) REVERT: c 145 LEU cc_start: 0.8257 (mt) cc_final: 0.7945 (mt) REVERT: c 152 ASN cc_start: 0.7854 (t0) cc_final: 0.7518 (t0) REVERT: c 153 TRP cc_start: 0.8661 (p-90) cc_final: 0.8176 (p-90) REVERT: c 159 CYS cc_start: 0.8301 (t) cc_final: 0.8033 (t) REVERT: c 167 TYR cc_start: 0.8098 (m-10) cc_final: 0.7192 (m-80) REVERT: c 168 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7662 (mt-10) REVERT: c 171 ASP cc_start: 0.8240 (m-30) cc_final: 0.7877 (m-30) REVERT: c 172 TRP cc_start: 0.8338 (t60) cc_final: 0.7746 (t60) REVERT: c 176 GLN cc_start: 0.8433 (pt0) cc_final: 0.8193 (pt0) REVERT: c 178 ARG cc_start: 0.7848 (ttm170) cc_final: 0.7615 (ttm170) outliers start: 0 outliers final: 0 residues processed: 762 average time/residue: 0.1519 time to fit residues: 164.4845 Evaluate side-chains 729 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 729 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 71 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 103 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 GLN ** B 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 54 HIS c 95 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.138813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.114144 restraints weight = 30475.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.118450 restraints weight = 16713.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.121287 restraints weight = 10512.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.123441 restraints weight = 7272.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.124710 restraints weight = 5391.887| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16108 Z= 0.169 Angle : 0.591 11.979 21822 Z= 0.309 Chirality : 0.046 0.210 2524 Planarity : 0.004 0.041 2752 Dihedral : 9.658 167.551 2154 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.20), residues: 1954 helix: 1.22 (0.18), residues: 806 sheet: 0.37 (0.27), residues: 386 loop : 1.05 (0.25), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 149 TYR 0.037 0.002 TYR M 399 PHE 0.029 0.002 PHE C 51 TRP 0.024 0.002 TRP c 172 HIS 0.004 0.001 HIS m 84 Details of bonding type rmsd covalent geometry : bond 0.00337 (16108) covalent geometry : angle 0.59070 (21822) hydrogen bonds : bond 0.04249 ( 815) hydrogen bonds : angle 5.03926 ( 2361) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 748 time to evaluate : 0.705 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: B 43 LYS cc_start: 0.8123 (mttt) cc_final: 0.7525 (mmmt) REVERT: B 47 LEU cc_start: 0.9030 (mt) cc_final: 0.8646 (mt) REVERT: B 50 MET cc_start: 0.8597 (mtm) cc_final: 0.8151 (mtm) REVERT: B 51 LEU cc_start: 0.8866 (mt) cc_final: 0.8498 (mt) REVERT: B 52 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7592 (mm-30) REVERT: B 54 ASN cc_start: 0.7960 (m110) cc_final: 0.7665 (m110) REVERT: B 59 LYS cc_start: 0.8814 (mtmm) cc_final: 0.8520 (mttp) REVERT: B 63 MET cc_start: 0.8513 (mmm) cc_final: 0.8042 (mmm) REVERT: B 66 ILE cc_start: 0.8527 (mm) cc_final: 0.8148 (mm) REVERT: B 72 LYS cc_start: 0.8867 (mmtt) cc_final: 0.8638 (ttmt) REVERT: B 74 LYS cc_start: 0.8630 (mmtt) cc_final: 0.8228 (mmtt) REVERT: B 80 PHE cc_start: 0.8523 (t80) cc_final: 0.7923 (t80) REVERT: B 85 LYS cc_start: 0.8601 (mttt) cc_final: 0.7774 (mttt) REVERT: B 90 LYS cc_start: 0.8475 (mttt) cc_final: 0.7651 (mmmm) REVERT: B 97 LEU cc_start: 0.8642 (mt) cc_final: 0.8200 (mm) REVERT: B 98 VAL cc_start: 0.8654 (t) cc_final: 0.8214 (p) REVERT: B 101 TYR cc_start: 0.8520 (t80) cc_final: 0.8301 (t80) REVERT: B 112 LEU cc_start: 0.8237 (mt) cc_final: 0.7568 (mp) REVERT: B 125 LYS cc_start: 0.8893 (mttt) cc_final: 0.8439 (mtpp) REVERT: B 128 ASN cc_start: 0.8220 (t0) cc_final: 0.8003 (t0) REVERT: B 132 ARG cc_start: 0.8269 (mtt180) cc_final: 0.7873 (mtm180) REVERT: B 147 ILE cc_start: 0.8377 (pt) cc_final: 0.7600 (pt) REVERT: B 151 MET cc_start: 0.7704 (mtp) cc_final: 0.6884 (mtp) REVERT: B 155 ILE cc_start: 0.9215 (mm) cc_final: 0.8958 (mm) REVERT: B 169 ASN cc_start: 0.8740 (m-40) cc_final: 0.8428 (m-40) REVERT: B 175 GLN cc_start: 0.8561 (tm-30) cc_final: 0.7843 (tm-30) REVERT: B 177 LEU cc_start: 0.8564 (tp) cc_final: 0.8342 (tp) REVERT: B 186 GLU cc_start: 0.8553 (pm20) cc_final: 0.8085 (pm20) REVERT: B 193 GLU cc_start: 0.8458 (tt0) cc_final: 0.8186 (tt0) REVERT: B 196 LEU cc_start: 0.8904 (mt) cc_final: 0.8571 (tp) REVERT: B 199 LYS cc_start: 0.8031 (mppt) cc_final: 0.7769 (mmtm) REVERT: B 202 LEU cc_start: 0.7461 (mm) cc_final: 0.7042 (tt) REVERT: B 207 VAL cc_start: 0.8752 (t) cc_final: 0.8407 (p) REVERT: B 213 GLU cc_start: 0.8173 (tt0) cc_final: 0.7736 (tt0) REVERT: B 215 CYS cc_start: 0.8640 (m) cc_final: 0.8384 (p) REVERT: B 228 LYS cc_start: 0.8654 (ttpt) cc_final: 0.8184 (ttpt) REVERT: B 244 ILE cc_start: 0.8995 (mt) cc_final: 0.8624 (tp) REVERT: B 247 MET cc_start: 0.7182 (tmm) cc_final: 0.6689 (tmm) REVERT: B 308 LEU cc_start: 0.8617 (mt) cc_final: 0.8274 (mm) REVERT: B 311 ARG cc_start: 0.8200 (ptt180) cc_final: 0.7565 (ptt-90) REVERT: B 317 MET cc_start: 0.8607 (tpp) cc_final: 0.8204 (tpp) REVERT: B 321 GLN cc_start: 0.8104 (tt0) cc_final: 0.7569 (tt0) REVERT: B 326 ILE cc_start: 0.8113 (mm) cc_final: 0.7837 (mm) REVERT: B 341 ARG cc_start: 0.8698 (ptt90) cc_final: 0.8283 (ptm-80) REVERT: B 387 THR cc_start: 0.8311 (m) cc_final: 0.7875 (m) REVERT: B 391 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7066 (mt-10) REVERT: B 417 ASP cc_start: 0.7997 (t0) cc_final: 0.7565 (m-30) REVERT: M 29 CYS cc_start: 0.8617 (t) cc_final: 0.8121 (t) REVERT: M 34 GLU cc_start: 0.8976 (tt0) cc_final: 0.8650 (tt0) REVERT: M 43 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7474 (mt-10) REVERT: M 77 LEU cc_start: 0.8555 (mt) cc_final: 0.8170 (mt) REVERT: M 78 PHE cc_start: 0.8772 (t80) cc_final: 0.8539 (t80) REVERT: M 88 ASP cc_start: 0.8396 (m-30) cc_final: 0.8046 (m-30) REVERT: M 89 THR cc_start: 0.8963 (m) cc_final: 0.8692 (p) REVERT: M 90 PHE cc_start: 0.8825 (m-10) cc_final: 0.8592 (m-10) REVERT: M 116 MET cc_start: 0.7839 (mtm) cc_final: 0.7568 (mtm) REVERT: M 123 LEU cc_start: 0.8617 (tp) cc_final: 0.8349 (tp) REVERT: M 126 GLU cc_start: 0.8165 (tp30) cc_final: 0.7606 (tp30) REVERT: M 128 ASN cc_start: 0.8299 (m-40) cc_final: 0.7932 (m-40) REVERT: M 131 LYS cc_start: 0.8517 (mtmm) cc_final: 0.7908 (mttp) REVERT: M 134 ILE cc_start: 0.8402 (mt) cc_final: 0.7617 (mt) REVERT: M 135 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8319 (mmtt) REVERT: M 157 LEU cc_start: 0.8488 (mt) cc_final: 0.8220 (mt) REVERT: M 161 GLN cc_start: 0.8354 (tp40) cc_final: 0.8123 (tp-100) REVERT: M 203 GLN cc_start: 0.7171 (mm-40) cc_final: 0.6880 (mm-40) REVERT: M 209 CYS cc_start: 0.7476 (t) cc_final: 0.6467 (m) REVERT: M 220 LEU cc_start: 0.8229 (mm) cc_final: 0.7831 (mm) REVERT: M 228 LEU cc_start: 0.8721 (mt) cc_final: 0.8074 (pp) REVERT: M 234 HIS cc_start: 0.8098 (t-90) cc_final: 0.7704 (t-90) REVERT: M 242 TRP cc_start: 0.7763 (t-100) cc_final: 0.7200 (t-100) REVERT: M 245 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6220 (mm-30) REVERT: M 262 TYR cc_start: 0.8390 (p90) cc_final: 0.8062 (p90) REVERT: M 298 LYS cc_start: 0.9010 (tttt) cc_final: 0.8616 (tttt) REVERT: M 300 ASN cc_start: 0.8994 (p0) cc_final: 0.8759 (p0) REVERT: M 377 PHE cc_start: 0.7827 (p90) cc_final: 0.7605 (p90) REVERT: M 393 ASP cc_start: 0.7834 (t0) cc_final: 0.7428 (t0) REVERT: M 402 PHE cc_start: 0.7736 (m-80) cc_final: 0.7137 (m-80) REVERT: M 414 PHE cc_start: 0.7833 (t80) cc_final: 0.7188 (t80) REVERT: C 18 MET cc_start: 0.6433 (mmm) cc_final: 0.6045 (mmm) REVERT: C 44 THR cc_start: 0.9106 (m) cc_final: 0.8703 (p) REVERT: C 64 THR cc_start: 0.6637 (m) cc_final: 0.6399 (t) REVERT: C 78 TRP cc_start: 0.8266 (m-10) cc_final: 0.7794 (m-10) REVERT: C 81 TYR cc_start: 0.7210 (m-80) cc_final: 0.6476 (m-80) REVERT: C 82 PHE cc_start: 0.7828 (m-10) cc_final: 0.7465 (m-80) REVERT: C 84 ASN cc_start: 0.8418 (t0) cc_final: 0.7651 (t0) REVERT: C 86 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7233 (mt0) REVERT: C 115 GLU cc_start: 0.8218 (tt0) cc_final: 0.7843 (tt0) REVERT: C 142 LYS cc_start: 0.8991 (mttm) cc_final: 0.8708 (mttm) REVERT: C 145 LEU cc_start: 0.8116 (mt) cc_final: 0.7814 (mt) REVERT: C 153 TRP cc_start: 0.8594 (p-90) cc_final: 0.7867 (p-90) REVERT: C 168 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7604 (mt-10) REVERT: C 172 TRP cc_start: 0.8321 (t60) cc_final: 0.7806 (t60) REVERT: C 178 ARG cc_start: 0.7883 (ttm170) cc_final: 0.7627 (ttm170) REVERT: b 43 LYS cc_start: 0.8224 (mttt) cc_final: 0.7656 (tttp) REVERT: b 45 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7352 (mm-30) REVERT: b 47 LEU cc_start: 0.8988 (mt) cc_final: 0.8584 (mt) REVERT: b 50 MET cc_start: 0.8393 (mtm) cc_final: 0.8148 (mtm) REVERT: b 51 LEU cc_start: 0.8892 (mt) cc_final: 0.8459 (mt) REVERT: b 59 LYS cc_start: 0.8689 (mtmm) cc_final: 0.8419 (mttp) REVERT: b 63 MET cc_start: 0.8672 (mmm) cc_final: 0.7972 (mmm) REVERT: b 66 ILE cc_start: 0.8407 (mm) cc_final: 0.8076 (mm) REVERT: b 80 PHE cc_start: 0.8406 (t80) cc_final: 0.7847 (t80) REVERT: b 102 LEU cc_start: 0.9040 (mt) cc_final: 0.8803 (mt) REVERT: b 107 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7458 (mt-10) REVERT: b 112 LEU cc_start: 0.8076 (mp) cc_final: 0.7308 (mp) REVERT: b 132 ARG cc_start: 0.8404 (mtt180) cc_final: 0.8115 (mtm180) REVERT: b 142 ILE cc_start: 0.9103 (mm) cc_final: 0.8899 (mp) REVERT: b 147 ILE cc_start: 0.8411 (pt) cc_final: 0.7594 (pt) REVERT: b 150 ILE cc_start: 0.8226 (mt) cc_final: 0.7974 (mt) REVERT: b 151 MET cc_start: 0.7526 (mtp) cc_final: 0.6847 (mtp) REVERT: b 152 MET cc_start: 0.8025 (tpt) cc_final: 0.7792 (tpt) REVERT: b 155 ILE cc_start: 0.9257 (mm) cc_final: 0.9037 (mm) REVERT: b 162 LEU cc_start: 0.7913 (mp) cc_final: 0.7097 (tp) REVERT: b 169 ASN cc_start: 0.8484 (m110) cc_final: 0.8251 (m-40) REVERT: b 186 GLU cc_start: 0.8329 (pm20) cc_final: 0.8110 (pm20) REVERT: b 187 MET cc_start: 0.8319 (mtm) cc_final: 0.7761 (mtm) REVERT: b 190 GLU cc_start: 0.7869 (pt0) cc_final: 0.7642 (pt0) REVERT: b 193 GLU cc_start: 0.8470 (tt0) cc_final: 0.8007 (tt0) REVERT: b 195 LEU cc_start: 0.9070 (mt) cc_final: 0.8703 (mt) REVERT: b 199 LYS cc_start: 0.8065 (mppt) cc_final: 0.7847 (mmtm) REVERT: b 202 LEU cc_start: 0.7688 (mm) cc_final: 0.7214 (tp) REVERT: b 207 VAL cc_start: 0.8816 (t) cc_final: 0.8432 (p) REVERT: b 209 MET cc_start: 0.7478 (tmm) cc_final: 0.7226 (tmm) REVERT: b 212 GLU cc_start: 0.8007 (tp30) cc_final: 0.7654 (tp30) REVERT: b 228 LYS cc_start: 0.8636 (ttpt) cc_final: 0.8217 (ttpt) REVERT: b 244 ILE cc_start: 0.9082 (mt) cc_final: 0.8662 (tp) REVERT: b 298 ARG cc_start: 0.8908 (mmm160) cc_final: 0.7364 (mpt180) REVERT: b 302 ARG cc_start: 0.8789 (ttm-80) cc_final: 0.8561 (ttm-80) REVERT: b 307 LEU cc_start: 0.8867 (mt) cc_final: 0.8413 (mt) REVERT: b 308 LEU cc_start: 0.8829 (mt) cc_final: 0.8537 (mm) REVERT: b 311 ARG cc_start: 0.8350 (ptt180) cc_final: 0.7762 (ptt-90) REVERT: b 317 MET cc_start: 0.8677 (tpp) cc_final: 0.8351 (tpp) REVERT: b 321 GLN cc_start: 0.8010 (tt0) cc_final: 0.7552 (tt0) REVERT: b 324 TRP cc_start: 0.8674 (t-100) cc_final: 0.7874 (t-100) REVERT: b 326 ILE cc_start: 0.8065 (mm) cc_final: 0.7792 (mm) REVERT: b 331 GLU cc_start: 0.7163 (mp0) cc_final: 0.6775 (mp0) REVERT: b 341 ARG cc_start: 0.8664 (ptt90) cc_final: 0.8305 (ptm-80) REVERT: b 360 MET cc_start: 0.8251 (ttm) cc_final: 0.6393 (ttm) REVERT: b 363 GLN cc_start: 0.8681 (mp-120) cc_final: 0.8462 (mp10) REVERT: b 367 MET cc_start: 0.6913 (mmp) cc_final: 0.6367 (mmt) REVERT: b 384 MET cc_start: 0.7870 (ptt) cc_final: 0.7411 (ptt) REVERT: b 386 LYS cc_start: 0.8445 (mtmt) cc_final: 0.8201 (mtpt) REVERT: b 417 ASP cc_start: 0.7724 (t0) cc_final: 0.7453 (t0) REVERT: b 627 ASN cc_start: 0.8641 (m110) cc_final: 0.8411 (m110) REVERT: m 1 MET cc_start: 0.6931 (mtt) cc_final: 0.6518 (mtt) REVERT: m 14 ILE cc_start: 0.8201 (tt) cc_final: 0.7979 (mt) REVERT: m 17 GLU cc_start: 0.7531 (pt0) cc_final: 0.7230 (pt0) REVERT: m 21 LYS cc_start: 0.7804 (mttt) cc_final: 0.6942 (mttm) REVERT: m 29 CYS cc_start: 0.8454 (m) cc_final: 0.7927 (t) REVERT: m 36 GLN cc_start: 0.8383 (tp-100) cc_final: 0.7990 (tp-100) REVERT: m 43 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7596 (mt-10) REVERT: m 44 ASN cc_start: 0.8325 (t0) cc_final: 0.7569 (t0) REVERT: m 45 VAL cc_start: 0.8855 (t) cc_final: 0.8594 (t) REVERT: m 71 GLN cc_start: 0.8326 (tp40) cc_final: 0.7939 (tp40) REVERT: m 74 VAL cc_start: 0.8986 (t) cc_final: 0.8694 (t) REVERT: m 77 LEU cc_start: 0.8610 (mt) cc_final: 0.8313 (mt) REVERT: m 78 PHE cc_start: 0.8798 (t80) cc_final: 0.8506 (t80) REVERT: m 80 ILE cc_start: 0.8594 (mt) cc_final: 0.8297 (mm) REVERT: m 108 ILE cc_start: 0.8841 (mt) cc_final: 0.8418 (mm) REVERT: m 111 GLU cc_start: 0.8090 (tt0) cc_final: 0.7751 (tt0) REVERT: m 116 MET cc_start: 0.7620 (mtm) cc_final: 0.7356 (mtm) REVERT: m 119 ASN cc_start: 0.8132 (t0) cc_final: 0.7446 (t0) REVERT: m 123 LEU cc_start: 0.8538 (tp) cc_final: 0.8328 (tp) REVERT: m 128 ASN cc_start: 0.8265 (m-40) cc_final: 0.7893 (m-40) REVERT: m 131 LYS cc_start: 0.8571 (mtmm) cc_final: 0.8261 (mttp) REVERT: m 134 ILE cc_start: 0.8331 (mt) cc_final: 0.8130 (tp) REVERT: m 140 LEU cc_start: 0.8480 (mt) cc_final: 0.8198 (tt) REVERT: m 141 ARG cc_start: 0.8144 (mmt90) cc_final: 0.7750 (mmt90) REVERT: m 186 GLU cc_start: 0.7428 (tt0) cc_final: 0.7210 (tt0) REVERT: m 209 CYS cc_start: 0.7420 (t) cc_final: 0.6536 (m) REVERT: m 220 LEU cc_start: 0.7942 (mm) cc_final: 0.7592 (mm) REVERT: m 234 HIS cc_start: 0.8119 (t-90) cc_final: 0.7760 (t-90) REVERT: m 240 LYS cc_start: 0.8611 (mttt) cc_final: 0.8022 (mmmm) REVERT: m 243 GLU cc_start: 0.8556 (tp30) cc_final: 0.8125 (tp30) REVERT: m 257 PHE cc_start: 0.8532 (p90) cc_final: 0.8261 (p90) REVERT: m 258 ARG cc_start: 0.8618 (mtp-110) cc_final: 0.8374 (mtm110) REVERT: m 262 TYR cc_start: 0.8174 (p90) cc_final: 0.7113 (p90) REVERT: m 298 LYS cc_start: 0.9082 (tttt) cc_final: 0.8660 (tttt) REVERT: m 299 GLN cc_start: 0.8282 (mt0) cc_final: 0.6840 (mt0) REVERT: m 393 ASP cc_start: 0.7948 (t0) cc_final: 0.7379 (t0) REVERT: m 402 PHE cc_start: 0.7816 (m-80) cc_final: 0.7431 (m-80) REVERT: m 406 LYS cc_start: 0.8494 (ttmt) cc_final: 0.8142 (ttmt) REVERT: m 407 TYR cc_start: 0.8356 (m-10) cc_final: 0.8087 (m-10) REVERT: m 414 PHE cc_start: 0.7905 (t80) cc_final: 0.7488 (t80) REVERT: c 30 LYS cc_start: 0.8466 (mttp) cc_final: 0.8111 (mttp) REVERT: c 44 THR cc_start: 0.9210 (m) cc_final: 0.8806 (p) REVERT: c 45 THR cc_start: 0.8839 (p) cc_final: 0.8631 (p) REVERT: c 53 VAL cc_start: 0.8446 (p) cc_final: 0.8197 (m) REVERT: c 58 TYR cc_start: 0.8209 (t80) cc_final: 0.7166 (t80) REVERT: c 64 THR cc_start: 0.6752 (m) cc_final: 0.6399 (t) REVERT: c 68 VAL cc_start: 0.8004 (t) cc_final: 0.7768 (p) REVERT: c 78 TRP cc_start: 0.8316 (m-10) cc_final: 0.7460 (m-10) REVERT: c 79 ARG cc_start: 0.8850 (ptm-80) cc_final: 0.8337 (mtm110) REVERT: c 82 PHE cc_start: 0.8025 (m-10) cc_final: 0.7598 (m-80) REVERT: c 84 ASN cc_start: 0.8306 (t0) cc_final: 0.7311 (t0) REVERT: c 110 MET cc_start: 0.8422 (mmm) cc_final: 0.7873 (mmm) REVERT: c 115 GLU cc_start: 0.7704 (tt0) cc_final: 0.7347 (tt0) REVERT: c 152 ASN cc_start: 0.7969 (t0) cc_final: 0.7650 (t0) REVERT: c 153 TRP cc_start: 0.8699 (p-90) cc_final: 0.8066 (p-90) REVERT: c 159 CYS cc_start: 0.8277 (t) cc_final: 0.7820 (t) REVERT: c 167 TYR cc_start: 0.8153 (m-10) cc_final: 0.7239 (m-80) REVERT: c 171 ASP cc_start: 0.8229 (m-30) cc_final: 0.7884 (m-30) REVERT: c 176 GLN cc_start: 0.8513 (pt0) cc_final: 0.8185 (pt0) REVERT: c 178 ARG cc_start: 0.7774 (ttm170) cc_final: 0.7526 (ttm170) outliers start: 0 outliers final: 0 residues processed: 748 average time/residue: 0.1527 time to fit residues: 161.9831 Evaluate side-chains 720 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 720 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 47 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 122 optimal weight: 0.1980 chunk 163 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 170 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN B 303 ASN B 363 GLN ** M 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 411 HIS b 355 GLN m 54 HIS m 380 GLN c 95 ASN c 128 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.136914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.112253 restraints weight = 30830.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.116529 restraints weight = 16909.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.119504 restraints weight = 10640.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.121606 restraints weight = 7355.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.122864 restraints weight = 5466.323| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16108 Z= 0.194 Angle : 0.616 8.153 21822 Z= 0.325 Chirality : 0.046 0.201 2524 Planarity : 0.004 0.043 2752 Dihedral : 9.725 165.837 2154 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.20), residues: 1954 helix: 1.16 (0.18), residues: 810 sheet: 0.40 (0.27), residues: 374 loop : 0.82 (0.25), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 149 TYR 0.028 0.002 TYR M 110 PHE 0.031 0.002 PHE m 121 TRP 0.025 0.002 TRP c 172 HIS 0.005 0.001 HIS b 624 Details of bonding type rmsd covalent geometry : bond 0.00373 (16108) covalent geometry : angle 0.61601 (21822) hydrogen bonds : bond 0.04455 ( 815) hydrogen bonds : angle 5.14884 ( 2361) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 766 time to evaluate : 0.640 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: B 43 LYS cc_start: 0.8132 (mttt) cc_final: 0.7516 (mmmt) REVERT: B 44 ASN cc_start: 0.8618 (m-40) cc_final: 0.8398 (m-40) REVERT: B 45 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7215 (mm-30) REVERT: B 47 LEU cc_start: 0.9055 (mt) cc_final: 0.8667 (mt) REVERT: B 48 LYS cc_start: 0.9178 (mtmt) cc_final: 0.8504 (mttt) REVERT: B 50 MET cc_start: 0.8612 (mtm) cc_final: 0.8197 (mtm) REVERT: B 51 LEU cc_start: 0.8830 (mt) cc_final: 0.8500 (mt) REVERT: B 52 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7594 (mm-30) REVERT: B 54 ASN cc_start: 0.7992 (m110) cc_final: 0.7642 (m110) REVERT: B 59 LYS cc_start: 0.8888 (mtmm) cc_final: 0.8596 (mttt) REVERT: B 60 LEU cc_start: 0.8874 (tp) cc_final: 0.8579 (tt) REVERT: B 63 MET cc_start: 0.8491 (mmm) cc_final: 0.8017 (mmm) REVERT: B 66 ILE cc_start: 0.8581 (mm) cc_final: 0.8241 (mm) REVERT: B 72 LYS cc_start: 0.8927 (mmtt) cc_final: 0.8583 (mtpt) REVERT: B 74 LYS cc_start: 0.8635 (mmtt) cc_final: 0.8148 (mmtt) REVERT: B 80 PHE cc_start: 0.8470 (t80) cc_final: 0.7783 (t80) REVERT: B 85 LYS cc_start: 0.8585 (mttt) cc_final: 0.7854 (mttt) REVERT: B 90 LYS cc_start: 0.8593 (mttt) cc_final: 0.7773 (mmmm) REVERT: B 97 LEU cc_start: 0.8643 (mt) cc_final: 0.8278 (mm) REVERT: B 101 TYR cc_start: 0.8596 (t80) cc_final: 0.8307 (t80) REVERT: B 107 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7521 (mt-10) REVERT: B 112 LEU cc_start: 0.8325 (mt) cc_final: 0.7539 (mp) REVERT: B 125 LYS cc_start: 0.8907 (mttt) cc_final: 0.8418 (mtpp) REVERT: B 128 ASN cc_start: 0.8363 (t0) cc_final: 0.8112 (t0) REVERT: B 132 ARG cc_start: 0.8238 (mtt180) cc_final: 0.7900 (mtm180) REVERT: B 147 ILE cc_start: 0.8380 (pt) cc_final: 0.7626 (pt) REVERT: B 151 MET cc_start: 0.7734 (mtp) cc_final: 0.6948 (mtp) REVERT: B 155 ILE cc_start: 0.9218 (mm) cc_final: 0.8955 (mm) REVERT: B 169 ASN cc_start: 0.8706 (m-40) cc_final: 0.8503 (m-40) REVERT: B 175 GLN cc_start: 0.8547 (tm-30) cc_final: 0.7797 (tm-30) REVERT: B 183 GLU cc_start: 0.8544 (mp0) cc_final: 0.8119 (mp0) REVERT: B 186 GLU cc_start: 0.8334 (pm20) cc_final: 0.8004 (pm20) REVERT: B 190 GLU cc_start: 0.8065 (tt0) cc_final: 0.7800 (tt0) REVERT: B 193 GLU cc_start: 0.8502 (tt0) cc_final: 0.8173 (tt0) REVERT: B 196 LEU cc_start: 0.8940 (mt) cc_final: 0.8399 (tt) REVERT: B 199 LYS cc_start: 0.8064 (mppt) cc_final: 0.7756 (mmtm) REVERT: B 202 LEU cc_start: 0.7710 (mm) cc_final: 0.7284 (tt) REVERT: B 207 VAL cc_start: 0.8742 (t) cc_final: 0.8359 (p) REVERT: B 213 GLU cc_start: 0.8176 (tt0) cc_final: 0.7708 (tt0) REVERT: B 215 CYS cc_start: 0.8924 (m) cc_final: 0.8429 (p) REVERT: B 228 LYS cc_start: 0.8698 (ttpt) cc_final: 0.8165 (ttpt) REVERT: B 244 ILE cc_start: 0.8987 (mt) cc_final: 0.8543 (tp) REVERT: B 246 HIS cc_start: 0.8360 (m-70) cc_final: 0.8124 (m-70) REVERT: B 247 MET cc_start: 0.7175 (tmm) cc_final: 0.6951 (tmm) REVERT: B 308 LEU cc_start: 0.8654 (mt) cc_final: 0.8278 (mm) REVERT: B 311 ARG cc_start: 0.8170 (ptt180) cc_final: 0.7532 (ptt-90) REVERT: B 317 MET cc_start: 0.8581 (tpp) cc_final: 0.8197 (tpp) REVERT: B 321 GLN cc_start: 0.8096 (tt0) cc_final: 0.7334 (tt0) REVERT: B 322 LEU cc_start: 0.8452 (tt) cc_final: 0.8170 (tt) REVERT: B 326 ILE cc_start: 0.8111 (mm) cc_final: 0.7840 (mm) REVERT: B 341 ARG cc_start: 0.8728 (ptt90) cc_final: 0.8276 (ptm-80) REVERT: B 363 GLN cc_start: 0.9000 (mm110) cc_final: 0.8783 (mp10) REVERT: B 383 THR cc_start: 0.8582 (p) cc_final: 0.8379 (p) REVERT: B 384 MET cc_start: 0.8111 (ptt) cc_final: 0.7383 (ptt) REVERT: B 388 LEU cc_start: 0.8799 (mm) cc_final: 0.8330 (mm) REVERT: B 391 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7079 (mt-10) REVERT: B 417 ASP cc_start: 0.8084 (t0) cc_final: 0.7636 (m-30) REVERT: B 631 THR cc_start: 0.8837 (m) cc_final: 0.8603 (t) REVERT: M 29 CYS cc_start: 0.8722 (t) cc_final: 0.8167 (t) REVERT: M 34 GLU cc_start: 0.8987 (tt0) cc_final: 0.8649 (tt0) REVERT: M 43 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7499 (mt-10) REVERT: M 44 ASN cc_start: 0.8263 (t0) cc_final: 0.7414 (t0) REVERT: M 72 THR cc_start: 0.8480 (p) cc_final: 0.8265 (p) REVERT: M 77 LEU cc_start: 0.8602 (mt) cc_final: 0.8225 (mt) REVERT: M 78 PHE cc_start: 0.8754 (t80) cc_final: 0.8532 (t80) REVERT: M 88 ASP cc_start: 0.8519 (m-30) cc_final: 0.8084 (m-30) REVERT: M 89 THR cc_start: 0.9085 (m) cc_final: 0.8861 (p) REVERT: M 114 GLU cc_start: 0.7789 (tp30) cc_final: 0.7146 (tp30) REVERT: M 116 MET cc_start: 0.7918 (mtm) cc_final: 0.7668 (mtm) REVERT: M 126 GLU cc_start: 0.8285 (tp30) cc_final: 0.7531 (tp30) REVERT: M 128 ASN cc_start: 0.8233 (m-40) cc_final: 0.7862 (m-40) REVERT: M 129 ILE cc_start: 0.8894 (mm) cc_final: 0.8599 (tp) REVERT: M 131 LYS cc_start: 0.8585 (mtmm) cc_final: 0.8189 (mttp) REVERT: M 135 LYS cc_start: 0.8834 (mmtt) cc_final: 0.8358 (mmtt) REVERT: M 157 LEU cc_start: 0.8496 (mt) cc_final: 0.8202 (mt) REVERT: M 161 GLN cc_start: 0.8358 (tp40) cc_final: 0.8155 (tp-100) REVERT: M 174 TYR cc_start: 0.7744 (m-80) cc_final: 0.7482 (m-80) REVERT: M 183 VAL cc_start: 0.8560 (t) cc_final: 0.8231 (p) REVERT: M 203 GLN cc_start: 0.7239 (mm-40) cc_final: 0.6760 (mm-40) REVERT: M 209 CYS cc_start: 0.7635 (t) cc_final: 0.6614 (m) REVERT: M 220 LEU cc_start: 0.8271 (mm) cc_final: 0.7908 (mm) REVERT: M 234 HIS cc_start: 0.8163 (t-90) cc_final: 0.7787 (t-90) REVERT: M 242 TRP cc_start: 0.7844 (t-100) cc_final: 0.7287 (t-100) REVERT: M 245 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6419 (mm-30) REVERT: M 257 PHE cc_start: 0.8199 (p90) cc_final: 0.7913 (p90) REVERT: M 258 ARG cc_start: 0.8260 (mtp180) cc_final: 0.7927 (mtm180) REVERT: M 298 LYS cc_start: 0.9038 (tttt) cc_final: 0.8616 (tttt) REVERT: M 393 ASP cc_start: 0.7852 (t0) cc_final: 0.7475 (t0) REVERT: M 414 PHE cc_start: 0.7840 (t80) cc_final: 0.7269 (t80) REVERT: C 64 THR cc_start: 0.6644 (m) cc_final: 0.6410 (t) REVERT: C 78 TRP cc_start: 0.8261 (m-10) cc_final: 0.7712 (m-10) REVERT: C 81 TYR cc_start: 0.7199 (m-80) cc_final: 0.6489 (m-80) REVERT: C 82 PHE cc_start: 0.7847 (m-10) cc_final: 0.7429 (m-80) REVERT: C 84 ASN cc_start: 0.8441 (t0) cc_final: 0.7728 (t0) REVERT: C 110 MET cc_start: 0.8402 (mmm) cc_final: 0.7957 (mmm) REVERT: C 115 GLU cc_start: 0.8245 (tt0) cc_final: 0.7838 (tt0) REVERT: C 142 LYS cc_start: 0.8996 (mttm) cc_final: 0.8736 (mttm) REVERT: C 168 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7590 (mt-10) REVERT: C 171 ASP cc_start: 0.8103 (m-30) cc_final: 0.7722 (m-30) REVERT: Y 411 HIS cc_start: 0.5532 (t-90) cc_final: 0.4725 (t-90) REVERT: b 43 LYS cc_start: 0.8146 (mttt) cc_final: 0.7660 (tptm) REVERT: b 47 LEU cc_start: 0.8995 (mt) cc_final: 0.8527 (mt) REVERT: b 50 MET cc_start: 0.8454 (mtm) cc_final: 0.8228 (mtm) REVERT: b 51 LEU cc_start: 0.8790 (mt) cc_final: 0.8356 (mt) REVERT: b 54 ASN cc_start: 0.8036 (m-40) cc_final: 0.7714 (m-40) REVERT: b 59 LYS cc_start: 0.8768 (mtmm) cc_final: 0.8455 (mttp) REVERT: b 63 MET cc_start: 0.8654 (mmm) cc_final: 0.7966 (mmm) REVERT: b 72 LYS cc_start: 0.8757 (mmtt) cc_final: 0.8466 (mmtt) REVERT: b 80 PHE cc_start: 0.8452 (t80) cc_final: 0.7782 (t80) REVERT: b 107 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7395 (mt-10) REVERT: b 112 LEU cc_start: 0.8136 (mp) cc_final: 0.7174 (mp) REVERT: b 121 GLN cc_start: 0.8152 (tt0) cc_final: 0.7841 (mt0) REVERT: b 124 LEU cc_start: 0.8972 (tp) cc_final: 0.8688 (tt) REVERT: b 132 ARG cc_start: 0.8422 (mtt180) cc_final: 0.8151 (mtm180) REVERT: b 142 ILE cc_start: 0.9105 (mm) cc_final: 0.8896 (mp) REVERT: b 147 ILE cc_start: 0.8417 (pt) cc_final: 0.7625 (pt) REVERT: b 150 ILE cc_start: 0.8240 (mt) cc_final: 0.7959 (mt) REVERT: b 151 MET cc_start: 0.7534 (mtp) cc_final: 0.6859 (mtp) REVERT: b 152 MET cc_start: 0.8024 (tpt) cc_final: 0.7808 (tpt) REVERT: b 155 ILE cc_start: 0.9262 (mm) cc_final: 0.9037 (mm) REVERT: b 162 LEU cc_start: 0.7880 (mp) cc_final: 0.7120 (tp) REVERT: b 181 ASP cc_start: 0.8403 (t0) cc_final: 0.8007 (t0) REVERT: b 187 MET cc_start: 0.8366 (mtm) cc_final: 0.7807 (mtm) REVERT: b 190 GLU cc_start: 0.7832 (pt0) cc_final: 0.7627 (pt0) REVERT: b 193 GLU cc_start: 0.8436 (tt0) cc_final: 0.8029 (tt0) REVERT: b 195 LEU cc_start: 0.9063 (mt) cc_final: 0.8708 (mt) REVERT: b 199 LYS cc_start: 0.8124 (mppt) cc_final: 0.7879 (mmtm) REVERT: b 202 LEU cc_start: 0.7818 (mm) cc_final: 0.7390 (tt) REVERT: b 207 VAL cc_start: 0.8825 (t) cc_final: 0.8429 (p) REVERT: b 212 GLU cc_start: 0.8047 (tp30) cc_final: 0.7710 (tp30) REVERT: b 218 ARG cc_start: 0.9025 (mtp-110) cc_final: 0.8765 (mtp85) REVERT: b 221 LEU cc_start: 0.9126 (mt) cc_final: 0.8924 (mt) REVERT: b 228 LYS cc_start: 0.8654 (ttpt) cc_final: 0.8240 (ttpt) REVERT: b 244 ILE cc_start: 0.9069 (mt) cc_final: 0.8647 (tp) REVERT: b 298 ARG cc_start: 0.8926 (mmm160) cc_final: 0.7922 (mpt180) REVERT: b 301 ILE cc_start: 0.8780 (mt) cc_final: 0.8524 (mt) REVERT: b 302 ARG cc_start: 0.8780 (ttm-80) cc_final: 0.8129 (mpt180) REVERT: b 307 LEU cc_start: 0.8894 (mt) cc_final: 0.8495 (mt) REVERT: b 308 LEU cc_start: 0.8856 (mt) cc_final: 0.8541 (mm) REVERT: b 311 ARG cc_start: 0.8329 (ptt180) cc_final: 0.7763 (ptt-90) REVERT: b 321 GLN cc_start: 0.8017 (tt0) cc_final: 0.7682 (tt0) REVERT: b 324 TRP cc_start: 0.8669 (t-100) cc_final: 0.8122 (t-100) REVERT: b 326 ILE cc_start: 0.8061 (mm) cc_final: 0.7762 (mm) REVERT: b 331 GLU cc_start: 0.7102 (mp0) cc_final: 0.6691 (mp0) REVERT: b 341 ARG cc_start: 0.8689 (ptt90) cc_final: 0.8310 (ptm-80) REVERT: b 346 ASN cc_start: 0.7544 (p0) cc_final: 0.7141 (p0) REVERT: b 360 MET cc_start: 0.8185 (ttm) cc_final: 0.6762 (ttm) REVERT: b 363 GLN cc_start: 0.8819 (mp-120) cc_final: 0.8564 (mp10) REVERT: b 367 MET cc_start: 0.7313 (mmp) cc_final: 0.6885 (mmt) REVERT: b 384 MET cc_start: 0.7921 (ptt) cc_final: 0.7435 (ptt) REVERT: b 640 PRO cc_start: 0.8626 (Cg_exo) cc_final: 0.8414 (Cg_endo) REVERT: m 1 MET cc_start: 0.6956 (mtt) cc_final: 0.6414 (mtt) REVERT: m 21 LYS cc_start: 0.7777 (mttt) cc_final: 0.6923 (mttm) REVERT: m 29 CYS cc_start: 0.8456 (m) cc_final: 0.7917 (t) REVERT: m 36 GLN cc_start: 0.8379 (tp-100) cc_final: 0.7986 (tp-100) REVERT: m 43 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7599 (mt-10) REVERT: m 44 ASN cc_start: 0.8370 (t0) cc_final: 0.7566 (t0) REVERT: m 45 VAL cc_start: 0.8903 (t) cc_final: 0.8672 (t) REVERT: m 71 GLN cc_start: 0.8339 (tp40) cc_final: 0.8065 (tp40) REVERT: m 78 PHE cc_start: 0.8799 (t80) cc_final: 0.8546 (t80) REVERT: m 80 ILE cc_start: 0.8570 (mt) cc_final: 0.8336 (mm) REVERT: m 88 ASP cc_start: 0.8375 (m-30) cc_final: 0.8122 (m-30) REVERT: m 90 PHE cc_start: 0.8768 (m-10) cc_final: 0.8516 (m-10) REVERT: m 96 GLU cc_start: 0.6599 (tm-30) cc_final: 0.6391 (tm-30) REVERT: m 108 ILE cc_start: 0.8902 (mt) cc_final: 0.8330 (mm) REVERT: m 111 GLU cc_start: 0.8101 (tt0) cc_final: 0.7833 (tt0) REVERT: m 119 ASN cc_start: 0.8074 (t0) cc_final: 0.7366 (t0) REVERT: m 126 GLU cc_start: 0.8304 (tp30) cc_final: 0.7663 (tp30) REVERT: m 128 ASN cc_start: 0.8251 (m-40) cc_final: 0.7442 (m-40) REVERT: m 131 LYS cc_start: 0.8596 (mtmm) cc_final: 0.8329 (mttt) REVERT: m 134 ILE cc_start: 0.8382 (mt) cc_final: 0.8099 (tp) REVERT: m 141 ARG cc_start: 0.8105 (mmt90) cc_final: 0.7782 (mmt90) REVERT: m 180 TYR cc_start: 0.6764 (m-10) cc_final: 0.6470 (m-10) REVERT: m 209 CYS cc_start: 0.7572 (t) cc_final: 0.6431 (m) REVERT: m 220 LEU cc_start: 0.8146 (mm) cc_final: 0.7855 (mm) REVERT: m 234 HIS cc_start: 0.8169 (t-90) cc_final: 0.7791 (t-90) REVERT: m 240 LYS cc_start: 0.8589 (mttt) cc_final: 0.8023 (mmmm) REVERT: m 242 TRP cc_start: 0.7727 (t-100) cc_final: 0.7484 (t-100) REVERT: m 243 GLU cc_start: 0.8582 (tp30) cc_final: 0.8143 (tp30) REVERT: m 257 PHE cc_start: 0.8504 (p90) cc_final: 0.8200 (p90) REVERT: m 258 ARG cc_start: 0.8661 (mtp-110) cc_final: 0.8149 (mtp-110) REVERT: m 262 TYR cc_start: 0.8144 (p90) cc_final: 0.7095 (p90) REVERT: m 272 ILE cc_start: 0.8028 (mm) cc_final: 0.7638 (tp) REVERT: m 393 ASP cc_start: 0.8076 (t0) cc_final: 0.7469 (t0) REVERT: m 402 PHE cc_start: 0.7800 (m-80) cc_final: 0.7414 (m-80) REVERT: m 407 TYR cc_start: 0.8281 (m-10) cc_final: 0.7853 (m-10) REVERT: m 414 PHE cc_start: 0.7899 (t80) cc_final: 0.7566 (t80) REVERT: c 30 LYS cc_start: 0.8493 (mttp) cc_final: 0.8140 (mttp) REVERT: c 53 VAL cc_start: 0.8434 (p) cc_final: 0.8149 (m) REVERT: c 58 TYR cc_start: 0.8269 (t80) cc_final: 0.7246 (t80) REVERT: c 64 THR cc_start: 0.6668 (m) cc_final: 0.6362 (t) REVERT: c 68 VAL cc_start: 0.8163 (t) cc_final: 0.7891 (p) REVERT: c 78 TRP cc_start: 0.8351 (m-10) cc_final: 0.7474 (m-10) REVERT: c 79 ARG cc_start: 0.8848 (ptm-80) cc_final: 0.8321 (mtm110) REVERT: c 82 PHE cc_start: 0.8012 (m-10) cc_final: 0.7487 (m-80) REVERT: c 84 ASN cc_start: 0.8274 (t0) cc_final: 0.7360 (t0) REVERT: c 110 MET cc_start: 0.8396 (mmm) cc_final: 0.7902 (mmm) REVERT: c 115 GLU cc_start: 0.7687 (tt0) cc_final: 0.7301 (tt0) REVERT: c 152 ASN cc_start: 0.8019 (t0) cc_final: 0.7707 (t0) REVERT: c 159 CYS cc_start: 0.8333 (t) cc_final: 0.7962 (t) REVERT: c 167 TYR cc_start: 0.8152 (m-10) cc_final: 0.7076 (m-10) REVERT: c 171 ASP cc_start: 0.8256 (m-30) cc_final: 0.7868 (m-30) REVERT: c 176 GLN cc_start: 0.8555 (pt0) cc_final: 0.8243 (pt0) REVERT: y 415 GLN cc_start: 0.7823 (mm110) cc_final: 0.7418 (mm110) outliers start: 0 outliers final: 0 residues processed: 766 average time/residue: 0.1527 time to fit residues: 166.1590 Evaluate side-chains 736 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 736 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 17 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN B 255 GLN B 355 GLN M 71 GLN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN b 231 ASN b 246 HIS b 355 GLN m 26 GLN m 128 ASN ** m 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 95 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.136612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.112283 restraints weight = 30749.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.116579 restraints weight = 16812.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.119483 restraints weight = 10530.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.121630 restraints weight = 7258.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.122783 restraints weight = 5372.443| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16108 Z= 0.186 Angle : 0.623 8.683 21822 Z= 0.327 Chirality : 0.047 0.221 2524 Planarity : 0.005 0.046 2752 Dihedral : 9.646 163.733 2154 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.20), residues: 1954 helix: 1.07 (0.18), residues: 818 sheet: 0.38 (0.27), residues: 382 loop : 0.75 (0.26), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 149 TYR 0.020 0.002 TYR B 105 PHE 0.025 0.002 PHE C 51 TRP 0.023 0.002 TRP c 172 HIS 0.012 0.001 HIS M 3 Details of bonding type rmsd covalent geometry : bond 0.00364 (16108) covalent geometry : angle 0.62260 (21822) hydrogen bonds : bond 0.04431 ( 815) hydrogen bonds : angle 5.17901 ( 2361) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 745 time to evaluate : 0.684 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: B 43 LYS cc_start: 0.8098 (mttt) cc_final: 0.7539 (tptt) REVERT: B 44 ASN cc_start: 0.8607 (m-40) cc_final: 0.8376 (m110) REVERT: B 45 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7134 (mm-30) REVERT: B 47 LEU cc_start: 0.9054 (mt) cc_final: 0.8606 (mt) REVERT: B 48 LYS cc_start: 0.9153 (mtmt) cc_final: 0.8522 (mttt) REVERT: B 50 MET cc_start: 0.8644 (mtm) cc_final: 0.8183 (mtm) REVERT: B 51 LEU cc_start: 0.8795 (mt) cc_final: 0.8454 (mt) REVERT: B 52 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7601 (mm-30) REVERT: B 54 ASN cc_start: 0.7989 (m110) cc_final: 0.7656 (m110) REVERT: B 59 LYS cc_start: 0.8852 (mtmm) cc_final: 0.8527 (mttp) REVERT: B 63 MET cc_start: 0.8561 (mmm) cc_final: 0.8114 (mmm) REVERT: B 72 LYS cc_start: 0.8914 (mmtt) cc_final: 0.8655 (ttmt) REVERT: B 74 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8128 (mmtt) REVERT: B 80 PHE cc_start: 0.8408 (t80) cc_final: 0.7897 (t80) REVERT: B 85 LYS cc_start: 0.8612 (mttt) cc_final: 0.7861 (mttt) REVERT: B 90 LYS cc_start: 0.8621 (mttt) cc_final: 0.7826 (mmmm) REVERT: B 97 LEU cc_start: 0.8747 (mt) cc_final: 0.8356 (mm) REVERT: B 101 TYR cc_start: 0.8548 (t80) cc_final: 0.8262 (t80) REVERT: B 107 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7488 (mt-10) REVERT: B 112 LEU cc_start: 0.8356 (mt) cc_final: 0.7768 (mt) REVERT: B 125 LYS cc_start: 0.8923 (mttt) cc_final: 0.8411 (mtpp) REVERT: B 128 ASN cc_start: 0.8408 (t0) cc_final: 0.8172 (t0) REVERT: B 132 ARG cc_start: 0.8244 (mtt180) cc_final: 0.7884 (mtm180) REVERT: B 137 ARG cc_start: 0.7827 (mtp-110) cc_final: 0.7540 (mtp-110) REVERT: B 147 ILE cc_start: 0.8372 (pt) cc_final: 0.7637 (pt) REVERT: B 151 MET cc_start: 0.7679 (mtp) cc_final: 0.6902 (mtp) REVERT: B 152 MET cc_start: 0.7935 (tpt) cc_final: 0.7729 (tpt) REVERT: B 155 ILE cc_start: 0.9191 (mm) cc_final: 0.8896 (mm) REVERT: B 169 ASN cc_start: 0.8704 (m-40) cc_final: 0.8450 (m-40) REVERT: B 175 GLN cc_start: 0.8540 (tm-30) cc_final: 0.7831 (tm-30) REVERT: B 183 GLU cc_start: 0.8550 (mp0) cc_final: 0.8135 (mp0) REVERT: B 186 GLU cc_start: 0.8311 (pm20) cc_final: 0.7977 (pm20) REVERT: B 190 GLU cc_start: 0.8105 (tt0) cc_final: 0.7809 (tt0) REVERT: B 193 GLU cc_start: 0.8500 (tt0) cc_final: 0.8183 (tt0) REVERT: B 196 LEU cc_start: 0.8883 (mt) cc_final: 0.8415 (tt) REVERT: B 199 LYS cc_start: 0.8065 (mppt) cc_final: 0.7762 (mmtm) REVERT: B 202 LEU cc_start: 0.7748 (mm) cc_final: 0.7325 (tt) REVERT: B 207 VAL cc_start: 0.8714 (t) cc_final: 0.8343 (p) REVERT: B 209 MET cc_start: 0.7591 (ttt) cc_final: 0.7287 (ttt) REVERT: B 213 GLU cc_start: 0.8190 (tt0) cc_final: 0.7742 (tt0) REVERT: B 215 CYS cc_start: 0.8973 (m) cc_final: 0.8362 (p) REVERT: B 228 LYS cc_start: 0.8675 (ttpt) cc_final: 0.8102 (ttpt) REVERT: B 244 ILE cc_start: 0.9019 (mt) cc_final: 0.8659 (tp) REVERT: B 246 HIS cc_start: 0.8372 (m-70) cc_final: 0.8171 (m-70) REVERT: B 247 MET cc_start: 0.7188 (tmm) cc_final: 0.6918 (tmm) REVERT: B 307 LEU cc_start: 0.8742 (mm) cc_final: 0.8309 (tp) REVERT: B 308 LEU cc_start: 0.8662 (mt) cc_final: 0.8277 (mm) REVERT: B 317 MET cc_start: 0.8577 (tpp) cc_final: 0.8168 (tpp) REVERT: B 321 GLN cc_start: 0.8104 (tt0) cc_final: 0.7371 (tt0) REVERT: B 326 ILE cc_start: 0.8085 (mm) cc_final: 0.7802 (mm) REVERT: B 341 ARG cc_start: 0.8753 (ptt90) cc_final: 0.8285 (ptm-80) REVERT: B 359 THR cc_start: 0.8018 (m) cc_final: 0.7805 (p) REVERT: B 383 THR cc_start: 0.8554 (p) cc_final: 0.8354 (p) REVERT: B 384 MET cc_start: 0.8072 (ptt) cc_final: 0.7373 (ptt) REVERT: B 388 LEU cc_start: 0.8785 (mm) cc_final: 0.8292 (mm) REVERT: B 391 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7067 (mt-10) REVERT: B 417 ASP cc_start: 0.8113 (t0) cc_final: 0.7644 (m-30) REVERT: M 1 MET cc_start: 0.6417 (mpp) cc_final: 0.6018 (mpp) REVERT: M 17 GLU cc_start: 0.7666 (pt0) cc_final: 0.7444 (pt0) REVERT: M 29 CYS cc_start: 0.8674 (t) cc_final: 0.8128 (t) REVERT: M 34 GLU cc_start: 0.8972 (tt0) cc_final: 0.8634 (tt0) REVERT: M 43 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7516 (mt-10) REVERT: M 44 ASN cc_start: 0.8270 (t0) cc_final: 0.7436 (t0) REVERT: M 63 LYS cc_start: 0.8402 (mttt) cc_final: 0.7563 (tmtt) REVERT: M 77 LEU cc_start: 0.8522 (mt) cc_final: 0.8146 (mt) REVERT: M 88 ASP cc_start: 0.8508 (m-30) cc_final: 0.8041 (m-30) REVERT: M 89 THR cc_start: 0.9183 (m) cc_final: 0.8879 (p) REVERT: M 116 MET cc_start: 0.8138 (mtm) cc_final: 0.7705 (mtm) REVERT: M 126 GLU cc_start: 0.8321 (tp30) cc_final: 0.7623 (tp30) REVERT: M 128 ASN cc_start: 0.8216 (m-40) cc_final: 0.7850 (m-40) REVERT: M 130 LEU cc_start: 0.8382 (tp) cc_final: 0.8067 (tp) REVERT: M 131 LYS cc_start: 0.8622 (mtmm) cc_final: 0.8231 (mttp) REVERT: M 135 LYS cc_start: 0.8851 (mmtt) cc_final: 0.8385 (mmtt) REVERT: M 174 TYR cc_start: 0.7759 (m-80) cc_final: 0.7494 (m-80) REVERT: M 183 VAL cc_start: 0.8586 (t) cc_final: 0.8205 (p) REVERT: M 209 CYS cc_start: 0.7654 (t) cc_final: 0.6559 (m) REVERT: M 220 LEU cc_start: 0.8192 (mm) cc_final: 0.7812 (mm) REVERT: M 234 HIS cc_start: 0.8214 (t-90) cc_final: 0.7856 (t-90) REVERT: M 242 TRP cc_start: 0.7874 (t-100) cc_final: 0.7269 (t-100) REVERT: M 245 GLU cc_start: 0.6806 (mm-30) cc_final: 0.6332 (mm-30) REVERT: M 257 PHE cc_start: 0.8197 (p90) cc_final: 0.7940 (p90) REVERT: M 258 ARG cc_start: 0.8303 (mtp180) cc_final: 0.7986 (mtm180) REVERT: M 262 TYR cc_start: 0.8424 (p90) cc_final: 0.8111 (p90) REVERT: M 298 LYS cc_start: 0.9056 (tttt) cc_final: 0.8611 (tttt) REVERT: M 310 VAL cc_start: 0.7517 (m) cc_final: 0.7187 (p) REVERT: M 345 LYS cc_start: 0.7660 (tptm) cc_final: 0.7451 (tptp) REVERT: M 393 ASP cc_start: 0.7810 (t0) cc_final: 0.7413 (t0) REVERT: M 414 PHE cc_start: 0.7828 (t80) cc_final: 0.7218 (t80) REVERT: C 44 THR cc_start: 0.9084 (m) cc_final: 0.8612 (p) REVERT: C 64 THR cc_start: 0.6586 (m) cc_final: 0.6342 (t) REVERT: C 78 TRP cc_start: 0.8278 (m-10) cc_final: 0.7715 (m-10) REVERT: C 81 TYR cc_start: 0.7183 (m-80) cc_final: 0.6437 (m-80) REVERT: C 82 PHE cc_start: 0.7908 (m-10) cc_final: 0.7529 (m-80) REVERT: C 84 ASN cc_start: 0.8463 (t0) cc_final: 0.7778 (t0) REVERT: C 108 MET cc_start: 0.7822 (mtm) cc_final: 0.7544 (mtt) REVERT: C 110 MET cc_start: 0.8505 (mmm) cc_final: 0.7948 (mmm) REVERT: C 115 GLU cc_start: 0.8180 (tt0) cc_final: 0.7751 (tt0) REVERT: C 142 LYS cc_start: 0.8998 (mttm) cc_final: 0.8775 (mttm) REVERT: C 145 LEU cc_start: 0.8149 (mt) cc_final: 0.7917 (mt) REVERT: C 168 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7584 (mt-10) REVERT: C 171 ASP cc_start: 0.7916 (m-30) cc_final: 0.7692 (m-30) REVERT: C 178 ARG cc_start: 0.7576 (ttm110) cc_final: 0.6986 (ttm110) REVERT: b 43 LYS cc_start: 0.8124 (mttt) cc_final: 0.7649 (tptm) REVERT: b 45 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7326 (mm-30) REVERT: b 47 LEU cc_start: 0.8971 (mt) cc_final: 0.8521 (mt) REVERT: b 48 LYS cc_start: 0.8916 (ptpp) cc_final: 0.7985 (pttm) REVERT: b 50 MET cc_start: 0.8513 (mtm) cc_final: 0.8251 (mtm) REVERT: b 51 LEU cc_start: 0.8755 (mt) cc_final: 0.8352 (mt) REVERT: b 59 LYS cc_start: 0.8738 (mtmm) cc_final: 0.8460 (mttp) REVERT: b 63 MET cc_start: 0.8731 (mmm) cc_final: 0.8019 (mmm) REVERT: b 72 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8469 (mmtt) REVERT: b 80 PHE cc_start: 0.8405 (t80) cc_final: 0.7874 (t80) REVERT: b 107 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7506 (mt-10) REVERT: b 112 LEU cc_start: 0.8091 (mp) cc_final: 0.7093 (mp) REVERT: b 124 LEU cc_start: 0.8936 (tp) cc_final: 0.8674 (tt) REVERT: b 132 ARG cc_start: 0.8409 (mtt180) cc_final: 0.8132 (mtm180) REVERT: b 147 ILE cc_start: 0.8378 (pt) cc_final: 0.7639 (pt) REVERT: b 151 MET cc_start: 0.7535 (mtp) cc_final: 0.6883 (mtp) REVERT: b 155 ILE cc_start: 0.9263 (mm) cc_final: 0.9061 (mm) REVERT: b 162 LEU cc_start: 0.7959 (mp) cc_final: 0.7142 (tp) REVERT: b 181 ASP cc_start: 0.8436 (t0) cc_final: 0.8041 (t0) REVERT: b 193 GLU cc_start: 0.8432 (tt0) cc_final: 0.8022 (tt0) REVERT: b 195 LEU cc_start: 0.9047 (mt) cc_final: 0.8822 (tt) REVERT: b 196 LEU cc_start: 0.9096 (tp) cc_final: 0.8883 (tp) REVERT: b 199 LYS cc_start: 0.8127 (mppt) cc_final: 0.7880 (mmtm) REVERT: b 202 LEU cc_start: 0.7856 (mm) cc_final: 0.7421 (tt) REVERT: b 207 VAL cc_start: 0.8806 (t) cc_final: 0.8600 (p) REVERT: b 209 MET cc_start: 0.7491 (tmm) cc_final: 0.7185 (tmm) REVERT: b 212 GLU cc_start: 0.8025 (tp30) cc_final: 0.6987 (tp30) REVERT: b 221 LEU cc_start: 0.9121 (mt) cc_final: 0.8901 (mt) REVERT: b 228 LYS cc_start: 0.8639 (ttpt) cc_final: 0.8234 (ttpt) REVERT: b 244 ILE cc_start: 0.9063 (mt) cc_final: 0.8404 (tp) REVERT: b 250 ARG cc_start: 0.7728 (ppt170) cc_final: 0.7206 (ptt90) REVERT: b 307 LEU cc_start: 0.8903 (mt) cc_final: 0.8601 (mt) REVERT: b 308 LEU cc_start: 0.8842 (mt) cc_final: 0.8525 (mm) REVERT: b 311 ARG cc_start: 0.8325 (ptt180) cc_final: 0.7727 (ptt-90) REVERT: b 317 MET cc_start: 0.8597 (tpp) cc_final: 0.8262 (tpp) REVERT: b 321 GLN cc_start: 0.7980 (tt0) cc_final: 0.7638 (tt0) REVERT: b 324 TRP cc_start: 0.8552 (t-100) cc_final: 0.8333 (t-100) REVERT: b 326 ILE cc_start: 0.8022 (mm) cc_final: 0.7747 (mm) REVERT: b 331 GLU cc_start: 0.7069 (mp0) cc_final: 0.6598 (mp0) REVERT: b 341 ARG cc_start: 0.8690 (ptt90) cc_final: 0.8181 (ptm-80) REVERT: b 360 MET cc_start: 0.8111 (ttm) cc_final: 0.7549 (ttm) REVERT: b 363 GLN cc_start: 0.8901 (mp-120) cc_final: 0.8698 (mp10) REVERT: b 367 MET cc_start: 0.7353 (mmp) cc_final: 0.7042 (mmp) REVERT: b 384 MET cc_start: 0.7783 (ptt) cc_final: 0.7238 (ptt) REVERT: b 385 ILE cc_start: 0.8634 (mm) cc_final: 0.8414 (mm) REVERT: b 629 LYS cc_start: 0.8350 (ttmt) cc_final: 0.8144 (ttmt) REVERT: b 640 PRO cc_start: 0.8582 (Cg_exo) cc_final: 0.8359 (Cg_endo) REVERT: m 1 MET cc_start: 0.6986 (mtt) cc_final: 0.6456 (mtt) REVERT: m 21 LYS cc_start: 0.7711 (mttt) cc_final: 0.6922 (mttm) REVERT: m 29 CYS cc_start: 0.8447 (m) cc_final: 0.7843 (t) REVERT: m 36 GLN cc_start: 0.8397 (tp-100) cc_final: 0.8009 (tp-100) REVERT: m 43 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7548 (mt-10) REVERT: m 44 ASN cc_start: 0.8398 (t0) cc_final: 0.7496 (t0) REVERT: m 45 VAL cc_start: 0.8904 (t) cc_final: 0.8649 (t) REVERT: m 71 GLN cc_start: 0.8316 (tp40) cc_final: 0.8017 (tp-100) REVERT: m 72 THR cc_start: 0.8524 (p) cc_final: 0.8296 (p) REVERT: m 74 VAL cc_start: 0.8980 (t) cc_final: 0.8677 (t) REVERT: m 78 PHE cc_start: 0.8801 (t80) cc_final: 0.8524 (t80) REVERT: m 80 ILE cc_start: 0.8574 (mt) cc_final: 0.8362 (mm) REVERT: m 88 ASP cc_start: 0.8296 (m-30) cc_final: 0.8058 (m-30) REVERT: m 96 GLU cc_start: 0.6476 (tm-30) cc_final: 0.6234 (tm-30) REVERT: m 108 ILE cc_start: 0.8887 (mt) cc_final: 0.8591 (mm) REVERT: m 119 ASN cc_start: 0.8077 (t0) cc_final: 0.7397 (t0) REVERT: m 126 GLU cc_start: 0.8258 (tp30) cc_final: 0.7628 (tp30) REVERT: m 128 ASN cc_start: 0.8253 (m110) cc_final: 0.7440 (m110) REVERT: m 131 LYS cc_start: 0.8613 (mtmm) cc_final: 0.8377 (mttt) REVERT: m 141 ARG cc_start: 0.8074 (mmt90) cc_final: 0.7766 (mmt90) REVERT: m 180 TYR cc_start: 0.6803 (m-10) cc_final: 0.6470 (m-10) REVERT: m 186 GLU cc_start: 0.7486 (tt0) cc_final: 0.7269 (tt0) REVERT: m 209 CYS cc_start: 0.7432 (t) cc_final: 0.6415 (m) REVERT: m 220 LEU cc_start: 0.8046 (mm) cc_final: 0.7680 (mm) REVERT: m 228 LEU cc_start: 0.8805 (mt) cc_final: 0.8360 (pp) REVERT: m 234 HIS cc_start: 0.8168 (t-90) cc_final: 0.7728 (t-90) REVERT: m 240 LYS cc_start: 0.8562 (mttt) cc_final: 0.7819 (mmmm) REVERT: m 242 TRP cc_start: 0.7767 (t-100) cc_final: 0.7488 (t-100) REVERT: m 243 GLU cc_start: 0.8572 (tp30) cc_final: 0.8183 (tp30) REVERT: m 257 PHE cc_start: 0.8487 (p90) cc_final: 0.8129 (p90) REVERT: m 258 ARG cc_start: 0.8659 (mtp-110) cc_final: 0.8182 (mtp-110) REVERT: m 272 ILE cc_start: 0.8071 (mm) cc_final: 0.7693 (tp) REVERT: m 342 ASP cc_start: 0.7899 (t0) cc_final: 0.7471 (t0) REVERT: m 393 ASP cc_start: 0.7979 (t0) cc_final: 0.7462 (t0) REVERT: m 402 PHE cc_start: 0.7804 (m-80) cc_final: 0.7390 (m-80) REVERT: m 403 LYS cc_start: 0.7445 (mppt) cc_final: 0.7170 (mppt) REVERT: m 406 LYS cc_start: 0.8672 (ttpt) cc_final: 0.8423 (ttpt) REVERT: m 407 TYR cc_start: 0.8116 (m-10) cc_final: 0.7655 (m-80) REVERT: m 414 PHE cc_start: 0.7841 (t80) cc_final: 0.7541 (t80) REVERT: c 30 LYS cc_start: 0.8486 (mttp) cc_final: 0.8134 (mttp) REVERT: c 53 VAL cc_start: 0.8425 (p) cc_final: 0.8152 (m) REVERT: c 58 TYR cc_start: 0.8215 (t80) cc_final: 0.7214 (t80) REVERT: c 64 THR cc_start: 0.6609 (m) cc_final: 0.6257 (t) REVERT: c 68 VAL cc_start: 0.8213 (t) cc_final: 0.7963 (p) REVERT: c 82 PHE cc_start: 0.7926 (m-10) cc_final: 0.7187 (m-80) REVERT: c 84 ASN cc_start: 0.8333 (t0) cc_final: 0.7402 (t0) REVERT: c 110 MET cc_start: 0.8406 (mmm) cc_final: 0.7916 (mmm) REVERT: c 115 GLU cc_start: 0.7784 (tt0) cc_final: 0.7504 (tt0) REVERT: c 167 TYR cc_start: 0.8103 (m-10) cc_final: 0.7031 (m-10) REVERT: c 171 ASP cc_start: 0.8252 (m-30) cc_final: 0.7904 (m-30) REVERT: y 415 GLN cc_start: 0.7779 (mm110) cc_final: 0.7375 (mm110) outliers start: 0 outliers final: 0 residues processed: 745 average time/residue: 0.1556 time to fit residues: 165.6003 Evaluate side-chains 733 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 733 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 58 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 149 optimal weight: 0.4980 chunk 145 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 129 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 143 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN ** M 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 376 GLN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 355 GLN m 26 GLN ** m 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 95 ASN c 128 GLN c 156 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.135597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.111217 restraints weight = 30688.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.115505 restraints weight = 16755.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.118538 restraints weight = 10534.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.120655 restraints weight = 7228.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.122216 restraints weight = 5318.241| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16108 Z= 0.153 Angle : 0.614 9.386 21822 Z= 0.321 Chirality : 0.046 0.171 2524 Planarity : 0.005 0.044 2752 Dihedral : 9.424 161.820 2154 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.20), residues: 1954 helix: 1.13 (0.18), residues: 820 sheet: 0.23 (0.27), residues: 388 loop : 0.80 (0.26), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 151 TYR 0.020 0.002 TYR M 110 PHE 0.029 0.002 PHE m 121 TRP 0.085 0.003 TRP c 172 HIS 0.018 0.001 HIS M 3 Details of bonding type rmsd covalent geometry : bond 0.00309 (16108) covalent geometry : angle 0.61383 (21822) hydrogen bonds : bond 0.04214 ( 815) hydrogen bonds : angle 5.07303 ( 2361) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 755 time to evaluate : 0.635 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: B 43 LYS cc_start: 0.8111 (mttt) cc_final: 0.7546 (tptt) REVERT: B 44 ASN cc_start: 0.8611 (m-40) cc_final: 0.8321 (m-40) REVERT: B 45 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7145 (mm-30) REVERT: B 47 LEU cc_start: 0.9055 (mt) cc_final: 0.8600 (mt) REVERT: B 48 LYS cc_start: 0.9152 (mtmt) cc_final: 0.8500 (mttt) REVERT: B 50 MET cc_start: 0.8618 (mtm) cc_final: 0.8131 (mtm) REVERT: B 51 LEU cc_start: 0.8761 (mt) cc_final: 0.8404 (mt) REVERT: B 52 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7599 (mm-30) REVERT: B 72 LYS cc_start: 0.8882 (mmtt) cc_final: 0.8629 (ttmt) REVERT: B 74 LYS cc_start: 0.8616 (mmtt) cc_final: 0.8120 (mmtt) REVERT: B 80 PHE cc_start: 0.8423 (t80) cc_final: 0.7877 (t80) REVERT: B 90 LYS cc_start: 0.8576 (mttt) cc_final: 0.7825 (mmmm) REVERT: B 101 TYR cc_start: 0.8554 (t80) cc_final: 0.8261 (t80) REVERT: B 107 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7428 (mt-10) REVERT: B 112 LEU cc_start: 0.8334 (mt) cc_final: 0.7698 (mt) REVERT: B 125 LYS cc_start: 0.8905 (mttt) cc_final: 0.8413 (mtpp) REVERT: B 128 ASN cc_start: 0.8279 (t0) cc_final: 0.8077 (t0) REVERT: B 137 ARG cc_start: 0.7782 (mtp-110) cc_final: 0.7444 (mtp-110) REVERT: B 147 ILE cc_start: 0.8354 (pt) cc_final: 0.7623 (pt) REVERT: B 151 MET cc_start: 0.7671 (mtp) cc_final: 0.6886 (mtp) REVERT: B 152 MET cc_start: 0.7916 (tpt) cc_final: 0.7700 (tpt) REVERT: B 155 ILE cc_start: 0.9179 (mm) cc_final: 0.8911 (mm) REVERT: B 169 ASN cc_start: 0.8693 (m-40) cc_final: 0.8432 (m-40) REVERT: B 175 GLN cc_start: 0.8519 (tm-30) cc_final: 0.7848 (tm-30) REVERT: B 181 ASP cc_start: 0.8506 (t0) cc_final: 0.7967 (t0) REVERT: B 183 GLU cc_start: 0.8498 (mp0) cc_final: 0.8248 (mp0) REVERT: B 187 MET cc_start: 0.8001 (pmm) cc_final: 0.7757 (pmm) REVERT: B 190 GLU cc_start: 0.8094 (tt0) cc_final: 0.7790 (tt0) REVERT: B 193 GLU cc_start: 0.8479 (tt0) cc_final: 0.8168 (tt0) REVERT: B 199 LYS cc_start: 0.8012 (mppt) cc_final: 0.7718 (mmtm) REVERT: B 202 LEU cc_start: 0.7547 (mm) cc_final: 0.7121 (tt) REVERT: B 207 VAL cc_start: 0.8679 (t) cc_final: 0.8311 (p) REVERT: B 209 MET cc_start: 0.7574 (ttt) cc_final: 0.7300 (ttt) REVERT: B 213 GLU cc_start: 0.8172 (tt0) cc_final: 0.7685 (tt0) REVERT: B 215 CYS cc_start: 0.9021 (m) cc_final: 0.8427 (p) REVERT: B 228 LYS cc_start: 0.8670 (ttpt) cc_final: 0.8138 (ttpt) REVERT: B 244 ILE cc_start: 0.9018 (mt) cc_final: 0.8614 (tp) REVERT: B 247 MET cc_start: 0.7136 (tmm) cc_final: 0.6890 (tmm) REVERT: B 307 LEU cc_start: 0.8693 (mm) cc_final: 0.8244 (tp) REVERT: B 308 LEU cc_start: 0.8658 (mt) cc_final: 0.8273 (mm) REVERT: B 311 ARG cc_start: 0.8063 (ptt180) cc_final: 0.7483 (ptt90) REVERT: B 317 MET cc_start: 0.8594 (tpp) cc_final: 0.8203 (tpp) REVERT: B 321 GLN cc_start: 0.8075 (tt0) cc_final: 0.7357 (tt0) REVERT: B 322 LEU cc_start: 0.8473 (tt) cc_final: 0.8188 (tt) REVERT: B 326 ILE cc_start: 0.8046 (mm) cc_final: 0.7762 (mm) REVERT: B 341 ARG cc_start: 0.8749 (ptt90) cc_final: 0.8282 (ptm-80) REVERT: B 383 THR cc_start: 0.8531 (p) cc_final: 0.8314 (p) REVERT: B 384 MET cc_start: 0.8064 (ptt) cc_final: 0.7384 (ptt) REVERT: B 388 LEU cc_start: 0.8763 (mm) cc_final: 0.8292 (mm) REVERT: B 391 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7096 (mt-10) REVERT: B 417 ASP cc_start: 0.8068 (t0) cc_final: 0.7610 (m-30) REVERT: B 631 THR cc_start: 0.8787 (m) cc_final: 0.8520 (t) REVERT: M 1 MET cc_start: 0.6261 (mpp) cc_final: 0.5974 (mpp) REVERT: M 29 CYS cc_start: 0.8610 (t) cc_final: 0.8108 (t) REVERT: M 34 GLU cc_start: 0.8979 (tt0) cc_final: 0.8636 (tt0) REVERT: M 43 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7621 (mt-10) REVERT: M 44 ASN cc_start: 0.8312 (t0) cc_final: 0.7555 (t0) REVERT: M 63 LYS cc_start: 0.8409 (mttt) cc_final: 0.7626 (tmtt) REVERT: M 72 THR cc_start: 0.8184 (p) cc_final: 0.7922 (p) REVERT: M 77 LEU cc_start: 0.8584 (mt) cc_final: 0.8228 (mt) REVERT: M 88 ASP cc_start: 0.8452 (m-30) cc_final: 0.8160 (m-30) REVERT: M 89 THR cc_start: 0.9184 (m) cc_final: 0.8887 (p) REVERT: M 111 GLU cc_start: 0.8146 (tt0) cc_final: 0.7720 (tt0) REVERT: M 116 MET cc_start: 0.8118 (mtm) cc_final: 0.7725 (mtm) REVERT: M 126 GLU cc_start: 0.8336 (tp30) cc_final: 0.7593 (tp30) REVERT: M 128 ASN cc_start: 0.8196 (m-40) cc_final: 0.7860 (m-40) REVERT: M 130 LEU cc_start: 0.8419 (tp) cc_final: 0.8163 (tp) REVERT: M 131 LYS cc_start: 0.8651 (mtmm) cc_final: 0.8194 (mttp) REVERT: M 134 ILE cc_start: 0.8407 (mt) cc_final: 0.8152 (mt) REVERT: M 135 LYS cc_start: 0.8813 (mmtt) cc_final: 0.8365 (mmtt) REVERT: M 174 TYR cc_start: 0.7720 (m-80) cc_final: 0.7472 (m-80) REVERT: M 183 VAL cc_start: 0.8556 (t) cc_final: 0.8173 (p) REVERT: M 209 CYS cc_start: 0.7610 (t) cc_final: 0.6643 (m) REVERT: M 220 LEU cc_start: 0.8213 (mm) cc_final: 0.7803 (mm) REVERT: M 234 HIS cc_start: 0.8172 (t-90) cc_final: 0.7767 (t-90) REVERT: M 242 TRP cc_start: 0.7914 (t-100) cc_final: 0.7291 (t-100) REVERT: M 245 GLU cc_start: 0.6690 (mm-30) cc_final: 0.6225 (mm-30) REVERT: M 257 PHE cc_start: 0.8169 (p90) cc_final: 0.7963 (p90) REVERT: M 258 ARG cc_start: 0.8336 (mtp180) cc_final: 0.7969 (mtm180) REVERT: M 262 TYR cc_start: 0.8403 (p90) cc_final: 0.8109 (p90) REVERT: M 298 LYS cc_start: 0.9028 (tttt) cc_final: 0.8647 (tttt) REVERT: M 310 VAL cc_start: 0.7551 (m) cc_final: 0.7231 (p) REVERT: M 377 PHE cc_start: 0.7729 (p90) cc_final: 0.7505 (p90) REVERT: M 393 ASP cc_start: 0.7778 (t0) cc_final: 0.7391 (t0) REVERT: M 414 PHE cc_start: 0.7886 (t80) cc_final: 0.7248 (t80) REVERT: C 78 TRP cc_start: 0.8296 (m-10) cc_final: 0.7724 (m-10) REVERT: C 81 TYR cc_start: 0.7103 (m-80) cc_final: 0.6804 (m-80) REVERT: C 82 PHE cc_start: 0.7816 (m-10) cc_final: 0.7377 (m-80) REVERT: C 84 ASN cc_start: 0.8455 (t0) cc_final: 0.7811 (t0) REVERT: C 108 MET cc_start: 0.7716 (mtm) cc_final: 0.7421 (mtt) REVERT: C 110 MET cc_start: 0.8420 (mmm) cc_final: 0.7859 (mmm) REVERT: C 115 GLU cc_start: 0.8100 (tt0) cc_final: 0.7690 (tt0) REVERT: C 145 LEU cc_start: 0.8164 (mt) cc_final: 0.7934 (mt) REVERT: C 151 ARG cc_start: 0.8527 (tpp-160) cc_final: 0.8067 (tpt170) REVERT: C 168 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7538 (mt-10) REVERT: C 171 ASP cc_start: 0.8044 (m-30) cc_final: 0.7658 (m-30) REVERT: C 178 ARG cc_start: 0.7375 (ttm110) cc_final: 0.6821 (ttm110) REVERT: b 43 LYS cc_start: 0.8075 (mttt) cc_final: 0.7648 (tptm) REVERT: b 47 LEU cc_start: 0.8988 (mt) cc_final: 0.8522 (mt) REVERT: b 50 MET cc_start: 0.8461 (mtm) cc_final: 0.8232 (mtm) REVERT: b 51 LEU cc_start: 0.8731 (mt) cc_final: 0.8303 (mt) REVERT: b 54 ASN cc_start: 0.8055 (m-40) cc_final: 0.7763 (m-40) REVERT: b 59 LYS cc_start: 0.8716 (mtmm) cc_final: 0.8466 (mttp) REVERT: b 63 MET cc_start: 0.8723 (mmm) cc_final: 0.8012 (mmm) REVERT: b 72 LYS cc_start: 0.8755 (mmtt) cc_final: 0.8474 (mmtt) REVERT: b 80 PHE cc_start: 0.8380 (t80) cc_final: 0.7949 (t80) REVERT: b 107 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7464 (mt-10) REVERT: b 112 LEU cc_start: 0.8183 (mp) cc_final: 0.7449 (mp) REVERT: b 121 GLN cc_start: 0.8075 (tt0) cc_final: 0.7815 (mt0) REVERT: b 124 LEU cc_start: 0.8900 (tp) cc_final: 0.8651 (tt) REVERT: b 132 ARG cc_start: 0.8319 (mtt180) cc_final: 0.8055 (mtm180) REVERT: b 147 ILE cc_start: 0.8380 (pt) cc_final: 0.7642 (pt) REVERT: b 150 ILE cc_start: 0.8261 (mt) cc_final: 0.8037 (mt) REVERT: b 151 MET cc_start: 0.7495 (mtp) cc_final: 0.6835 (mtp) REVERT: b 152 MET cc_start: 0.8020 (tpt) cc_final: 0.7813 (tpt) REVERT: b 162 LEU cc_start: 0.7987 (mp) cc_final: 0.7189 (tp) REVERT: b 181 ASP cc_start: 0.8416 (t0) cc_final: 0.7971 (t0) REVERT: b 195 LEU cc_start: 0.9010 (mt) cc_final: 0.8788 (tt) REVERT: b 196 LEU cc_start: 0.9088 (tp) cc_final: 0.8732 (tp) REVERT: b 199 LYS cc_start: 0.8071 (mppt) cc_final: 0.7834 (mmtm) REVERT: b 202 LEU cc_start: 0.7775 (mm) cc_final: 0.7312 (tt) REVERT: b 212 GLU cc_start: 0.7986 (tp30) cc_final: 0.7001 (tp30) REVERT: b 225 ASN cc_start: 0.8077 (m-40) cc_final: 0.7124 (m-40) REVERT: b 228 LYS cc_start: 0.8624 (ttpt) cc_final: 0.8264 (ttpt) REVERT: b 237 GLU cc_start: 0.7633 (tt0) cc_final: 0.7146 (tt0) REVERT: b 241 GLN cc_start: 0.8054 (mt0) cc_final: 0.7503 (mt0) REVERT: b 250 ARG cc_start: 0.7745 (ppt170) cc_final: 0.7251 (ptt90) REVERT: b 307 LEU cc_start: 0.8875 (mt) cc_final: 0.8455 (mt) REVERT: b 308 LEU cc_start: 0.8825 (mt) cc_final: 0.8508 (mm) REVERT: b 311 ARG cc_start: 0.8304 (ptt180) cc_final: 0.7723 (ptt-90) REVERT: b 317 MET cc_start: 0.8594 (tpp) cc_final: 0.8271 (tpp) REVERT: b 321 GLN cc_start: 0.8061 (tt0) cc_final: 0.7442 (tt0) REVERT: b 326 ILE cc_start: 0.7990 (mm) cc_final: 0.7724 (mm) REVERT: b 331 GLU cc_start: 0.7073 (mp0) cc_final: 0.6618 (mp0) REVERT: b 346 ASN cc_start: 0.7530 (p0) cc_final: 0.7111 (p0) REVERT: b 364 ARG cc_start: 0.6678 (mtt90) cc_final: 0.6337 (mpp80) REVERT: b 367 MET cc_start: 0.7301 (mmp) cc_final: 0.7076 (mmp) REVERT: b 384 MET cc_start: 0.7660 (ptt) cc_final: 0.7173 (ptt) REVERT: b 629 LYS cc_start: 0.8368 (ttmt) cc_final: 0.8159 (ttmt) REVERT: b 631 THR cc_start: 0.8960 (m) cc_final: 0.8736 (t) REVERT: b 640 PRO cc_start: 0.8576 (Cg_exo) cc_final: 0.8356 (Cg_endo) REVERT: m 1 MET cc_start: 0.7035 (mtt) cc_final: 0.6469 (mtt) REVERT: m 21 LYS cc_start: 0.7675 (mttt) cc_final: 0.7395 (mttp) REVERT: m 29 CYS cc_start: 0.8499 (m) cc_final: 0.7898 (t) REVERT: m 36 GLN cc_start: 0.8371 (tp-100) cc_final: 0.7995 (tp-100) REVERT: m 43 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7522 (mt-10) REVERT: m 44 ASN cc_start: 0.8318 (t0) cc_final: 0.7519 (t0) REVERT: m 45 VAL cc_start: 0.8883 (t) cc_final: 0.8647 (t) REVERT: m 67 VAL cc_start: 0.8224 (t) cc_final: 0.7837 (m) REVERT: m 71 GLN cc_start: 0.8287 (tp40) cc_final: 0.7899 (tp-100) REVERT: m 72 THR cc_start: 0.8486 (p) cc_final: 0.8241 (p) REVERT: m 74 VAL cc_start: 0.8978 (t) cc_final: 0.8673 (t) REVERT: m 78 PHE cc_start: 0.8743 (t80) cc_final: 0.8520 (t80) REVERT: m 80 ILE cc_start: 0.8564 (mt) cc_final: 0.8327 (mm) REVERT: m 82 PHE cc_start: 0.8290 (t80) cc_final: 0.7902 (t80) REVERT: m 88 ASP cc_start: 0.8297 (m-30) cc_final: 0.8018 (m-30) REVERT: m 96 GLU cc_start: 0.6463 (tm-30) cc_final: 0.6191 (tm-30) REVERT: m 108 ILE cc_start: 0.8874 (mt) cc_final: 0.8604 (mm) REVERT: m 111 GLU cc_start: 0.8112 (tt0) cc_final: 0.7680 (tt0) REVERT: m 126 GLU cc_start: 0.8326 (tp30) cc_final: 0.7626 (tp30) REVERT: m 128 ASN cc_start: 0.8361 (m110) cc_final: 0.7577 (m110) REVERT: m 131 LYS cc_start: 0.8599 (mtmm) cc_final: 0.8340 (mttt) REVERT: m 134 ILE cc_start: 0.8167 (mt) cc_final: 0.7817 (tt) REVERT: m 140 LEU cc_start: 0.8470 (mt) cc_final: 0.8222 (tt) REVERT: m 141 ARG cc_start: 0.8074 (mmt90) cc_final: 0.7694 (mmt90) REVERT: m 180 TYR cc_start: 0.6799 (m-10) cc_final: 0.6433 (m-10) REVERT: m 209 CYS cc_start: 0.7523 (t) cc_final: 0.6455 (m) REVERT: m 220 LEU cc_start: 0.8011 (mm) cc_final: 0.7642 (mm) REVERT: m 228 LEU cc_start: 0.8790 (mt) cc_final: 0.8385 (pp) REVERT: m 234 HIS cc_start: 0.8148 (t-90) cc_final: 0.7770 (t-90) REVERT: m 240 LYS cc_start: 0.8532 (mttt) cc_final: 0.7795 (mmmm) REVERT: m 243 GLU cc_start: 0.8544 (tp30) cc_final: 0.8126 (tp30) REVERT: m 257 PHE cc_start: 0.8506 (p90) cc_final: 0.8198 (p90) REVERT: m 258 ARG cc_start: 0.8660 (mtp-110) cc_final: 0.8178 (mtp-110) REVERT: m 272 ILE cc_start: 0.8047 (mm) cc_final: 0.7026 (tp) REVERT: m 342 ASP cc_start: 0.7794 (t0) cc_final: 0.7376 (t0) REVERT: m 378 LYS cc_start: 0.7857 (ptmm) cc_final: 0.7441 (ptmm) REVERT: m 393 ASP cc_start: 0.7954 (t0) cc_final: 0.7351 (t0) REVERT: m 403 LYS cc_start: 0.7487 (mppt) cc_final: 0.7183 (mppt) REVERT: m 406 LYS cc_start: 0.8618 (ttpt) cc_final: 0.8322 (ttpt) REVERT: m 407 TYR cc_start: 0.8039 (m-10) cc_final: 0.7556 (m-80) REVERT: m 414 PHE cc_start: 0.7877 (t80) cc_final: 0.7426 (t80) REVERT: c 30 LYS cc_start: 0.8444 (mttp) cc_final: 0.8069 (mttp) REVERT: c 53 VAL cc_start: 0.8438 (p) cc_final: 0.8120 (m) REVERT: c 64 THR cc_start: 0.6563 (m) cc_final: 0.6238 (t) REVERT: c 68 VAL cc_start: 0.8160 (t) cc_final: 0.7916 (p) REVERT: c 78 TRP cc_start: 0.8333 (m-10) cc_final: 0.7408 (m-10) REVERT: c 84 ASN cc_start: 0.8322 (t0) cc_final: 0.7418 (t0) REVERT: c 110 MET cc_start: 0.8356 (mmm) cc_final: 0.7831 (mmm) REVERT: c 115 GLU cc_start: 0.7857 (tt0) cc_final: 0.7482 (tt0) REVERT: c 116 LEU cc_start: 0.7869 (mt) cc_final: 0.7603 (mt) REVERT: c 145 LEU cc_start: 0.8283 (mt) cc_final: 0.8015 (mt) REVERT: c 153 TRP cc_start: 0.8613 (p-90) cc_final: 0.8082 (p-90) REVERT: c 159 CYS cc_start: 0.8274 (t) cc_final: 0.8015 (t) REVERT: c 171 ASP cc_start: 0.8237 (m-30) cc_final: 0.7811 (m-30) REVERT: c 172 TRP cc_start: 0.8139 (t60) cc_final: 0.7415 (t60) REVERT: y 411 HIS cc_start: 0.6330 (t-90) cc_final: 0.5654 (t-170) REVERT: y 415 GLN cc_start: 0.7786 (mm110) cc_final: 0.7411 (mm110) outliers start: 0 outliers final: 0 residues processed: 755 average time/residue: 0.1421 time to fit residues: 153.5747 Evaluate side-chains 731 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 731 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 137 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 117 optimal weight: 0.6980 chunk 149 optimal weight: 0.6980 chunk 50 optimal weight: 0.1980 chunk 29 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN B 321 GLN B 355 GLN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 411 HIS b 231 ASN b 355 GLN m 26 GLN m 203 GLN ** m 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 84 ASN c 95 ASN c 128 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.137292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.113034 restraints weight = 30412.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.117294 restraints weight = 16566.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.120239 restraints weight = 10399.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.122304 restraints weight = 7142.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.123875 restraints weight = 5281.859| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.5777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16108 Z= 0.144 Angle : 0.604 9.124 21822 Z= 0.314 Chirality : 0.046 0.191 2524 Planarity : 0.005 0.045 2752 Dihedral : 9.264 160.740 2154 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.20), residues: 1954 helix: 1.19 (0.18), residues: 822 sheet: 0.21 (0.27), residues: 388 loop : 0.74 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG m 61 TYR 0.024 0.002 TYR c 58 PHE 0.022 0.002 PHE C 51 TRP 0.074 0.003 TRP c 172 HIS 0.010 0.001 HIS M 3 Details of bonding type rmsd covalent geometry : bond 0.00292 (16108) covalent geometry : angle 0.60393 (21822) hydrogen bonds : bond 0.04072 ( 815) hydrogen bonds : angle 4.99336 ( 2361) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3645.31 seconds wall clock time: 63 minutes 34.00 seconds (3814.00 seconds total)