Starting phenix.real_space_refine on Sat Jun 14 06:17:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c5a_45209/06_2025/9c5a_45209.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c5a_45209/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9c5a_45209/06_2025/9c5a_45209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c5a_45209/06_2025/9c5a_45209.map" model { file = "/net/cci-nas-00/data/ceres_data/9c5a_45209/06_2025/9c5a_45209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c5a_45209/06_2025/9c5a_45209.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: c, b, m, Y Time building chain proxies: 11.68, per 1000 atoms: 0.74 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: 3.51 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.87 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: 4.76 Time building geometry restraints manager: 4.18 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: 0.08 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'M' selection = chain 'm' } 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: 4.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 37.180 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.160 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.025 0.005 TRP C 153 HIS 0.008 0.002 HIS b 624 PHE 0.025 0.004 PHE C 124 TYR 0.033 0.005 TYR M 275 ARG 0.007 0.001 ARG B 132 Details of bonding type rmsd hydrogen bonds : bond 0.17054 ( 815) hydrogen bonds : angle 7.97942 ( 2361) covalent geometry : bond 0.01406 (16108) covalent geometry : angle 1.48497 (21822) *********************** 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 : 1.757 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: 0.3046 time to fit residues: 360.9903 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 : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 0.0060 chunk 113 optimal weight: 0.5980 chunk 176 optimal weight: 3.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 ** 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 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** ** c 176 GLN ** 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 = 0.3828 r_free = 0.3828 target = 0.139179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.115032 restraints weight = 31067.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.119392 restraints weight = 16547.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.122351 restraints weight = 10199.735| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16108 Z= 0.186 Angle : 0.663 7.954 21822 Z= 0.357 Chirality : 0.047 0.171 2524 Planarity : 0.005 0.058 2752 Dihedral : 11.395 177.967 2154 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.17 % Allowed : 1.36 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.20), residues: 1954 helix: 0.74 (0.18), residues: 818 sheet: 0.02 (0.27), residues: 360 loop : 1.40 (0.25), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP m 242 HIS 0.017 0.001 HIS m 278 PHE 0.015 0.002 PHE B 211 TYR 0.022 0.003 TYR M 180 ARG 0.005 0.001 ARG c 79 Details of bonding type rmsd hydrogen bonds : bond 0.05604 ( 815) hydrogen bonds : angle 5.91504 ( 2361) covalent geometry : bond 0.00365 (16108) covalent geometry : angle 0.66282 (21822) *********************** 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 806 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 803 time to evaluate : 1.617 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: B 43 LYS cc_start: 0.8294 (mttt) cc_final: 0.7623 (mmmt) REVERT: B 45 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7431 (mm-30) REVERT: B 48 LYS cc_start: 0.8919 (mtmt) cc_final: 0.8513 (mtmm) REVERT: B 50 MET cc_start: 0.8652 (mtm) cc_final: 0.8270 (mtm) REVERT: B 54 ASN cc_start: 0.7594 (p0) cc_final: 0.7024 (t0) REVERT: B 55 LYS cc_start: 0.8411 (ttpt) cc_final: 0.7914 (mtpt) REVERT: B 63 MET cc_start: 0.8513 (mmm) cc_final: 0.7761 (mmm) REVERT: B 64 LYS cc_start: 0.8944 (mttt) cc_final: 0.8441 (mtpp) REVERT: B 72 LYS cc_start: 0.8796 (mmtt) cc_final: 0.8451 (mtmt) REVERT: B 74 LYS cc_start: 0.8638 (mmtt) cc_final: 0.8374 (mmtt) REVERT: B 79 LEU cc_start: 0.8497 (mt) cc_final: 0.8280 (mt) REVERT: B 83 VAL cc_start: 0.8394 (t) cc_final: 0.7998 (t) REVERT: B 85 LYS cc_start: 0.8679 (mttt) cc_final: 0.8368 (mttt) REVERT: B 90 LYS cc_start: 0.8246 (mttt) cc_final: 0.7869 (mttt) REVERT: B 101 TYR cc_start: 0.8528 (t80) cc_final: 0.8177 (t80) REVERT: B 104 ARG cc_start: 0.8620 (tpt90) cc_final: 0.8373 (tpt90) REVERT: B 125 LYS cc_start: 0.8755 (mttt) cc_final: 0.8355 (mtpp) REVERT: B 132 ARG cc_start: 0.8400 (mtt180) cc_final: 0.8117 (ttm170) REVERT: B 139 LEU cc_start: 0.8413 (tp) cc_final: 0.8183 (tt) REVERT: B 141 SER cc_start: 0.8426 (m) cc_final: 0.8175 (m) REVERT: B 142 ILE cc_start: 0.8958 (mm) cc_final: 0.8615 (mp) REVERT: B 151 MET cc_start: 0.7961 (mtp) cc_final: 0.7665 (mtp) REVERT: B 166 VAL cc_start: 0.8656 (t) cc_final: 0.8427 (p) REVERT: B 190 GLU cc_start: 0.8213 (tt0) cc_final: 0.7997 (tt0) REVERT: B 191 VAL cc_start: 0.9033 (t) cc_final: 0.8792 (p) REVERT: B 193 GLU cc_start: 0.8428 (tt0) cc_final: 0.8181 (tt0) REVERT: B 196 LEU cc_start: 0.8547 (mt) cc_final: 0.8263 (tp) REVERT: B 202 LEU cc_start: 0.7771 (mm) cc_final: 0.7332 (tp) REVERT: B 207 VAL cc_start: 0.8942 (t) cc_final: 0.8620 (p) REVERT: B 215 CYS cc_start: 0.8175 (t) cc_final: 0.7962 (t) REVERT: B 244 ILE cc_start: 0.9060 (mt) cc_final: 0.8717 (tp) REVERT: B 246 HIS cc_start: 0.8329 (m-70) cc_final: 0.8127 (m-70) REVERT: B 247 MET cc_start: 0.7505 (tmm) cc_final: 0.7098 (tmm) REVERT: B 298 ARG cc_start: 0.8516 (mmm160) cc_final: 0.7787 (mpt180) REVERT: B 305 LYS cc_start: 0.8756 (tttt) cc_final: 0.8274 (ttpp) REVERT: B 308 LEU cc_start: 0.8531 (mt) cc_final: 0.8267 (mm) REVERT: B 311 ARG cc_start: 0.8405 (ptt180) cc_final: 0.7755 (ptt-90) REVERT: B 321 GLN cc_start: 0.7951 (tt0) cc_final: 0.7672 (tt0) REVERT: B 322 LEU cc_start: 0.8436 (tt) cc_final: 0.8201 (tt) REVERT: B 324 TRP cc_start: 0.8785 (t-100) cc_final: 0.8521 (t-100) REVERT: B 326 ILE cc_start: 0.8006 (mm) cc_final: 0.7701 (mm) REVERT: B 341 ARG cc_start: 0.8739 (ptt90) cc_final: 0.8325 (ptm-80) REVERT: B 349 VAL cc_start: 0.8301 (t) cc_final: 0.8096 (t) REVERT: B 387 THR cc_start: 0.8466 (m) cc_final: 0.8180 (m) REVERT: B 388 LEU cc_start: 0.8628 (mt) cc_final: 0.8397 (mm) REVERT: B 391 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7049 (mt-10) REVERT: B 417 ASP cc_start: 0.8064 (t0) cc_final: 0.7822 (t0) REVERT: M 1 MET cc_start: 0.6775 (mtt) cc_final: 0.6461 (mtt) REVERT: M 17 GLU cc_start: 0.7752 (pt0) cc_final: 0.7473 (pt0) REVERT: M 21 LYS cc_start: 0.8126 (mttt) cc_final: 0.7279 (mtpp) REVERT: M 30 ASP cc_start: 0.8298 (m-30) cc_final: 0.8075 (t0) REVERT: M 43 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7459 (mt-10) REVERT: M 64 LEU cc_start: 0.8394 (tp) cc_final: 0.8187 (tp) REVERT: M 67 VAL cc_start: 0.8207 (t) cc_final: 0.7888 (m) REVERT: M 71 GLN cc_start: 0.8368 (tp40) cc_final: 0.8078 (tp-100) REVERT: M 74 VAL cc_start: 0.8880 (t) cc_final: 0.8457 (p) REVERT: M 78 PHE cc_start: 0.8875 (t80) cc_final: 0.8554 (t80) REVERT: M 89 THR cc_start: 0.8888 (m) cc_final: 0.8426 (p) REVERT: M 92 ASP cc_start: 0.7753 (t0) cc_final: 0.7421 (t0) REVERT: M 96 GLU cc_start: 0.6824 (tm-30) cc_final: 0.6608 (tm-30) REVERT: M 115 GLU cc_start: 0.8242 (mm-30) cc_final: 0.8014 (tp30) REVERT: M 116 MET cc_start: 0.7828 (mtm) cc_final: 0.7336 (mtm) REVERT: M 119 ASN cc_start: 0.8394 (t0) cc_final: 0.7786 (t0) REVERT: M 121 PHE cc_start: 0.7655 (t80) cc_final: 0.7202 (t80) REVERT: M 126 GLU cc_start: 0.8134 (tp30) cc_final: 0.7474 (tp30) REVERT: M 128 ASN cc_start: 0.8639 (m-40) cc_final: 0.7881 (m110) REVERT: M 131 LYS cc_start: 0.8566 (mttp) cc_final: 0.8060 (mttt) REVERT: M 134 ILE cc_start: 0.8408 (mt) cc_final: 0.7923 (mt) REVERT: M 135 LYS cc_start: 0.8867 (mmtt) cc_final: 0.8346 (mmtt) REVERT: M 153 VAL cc_start: 0.7890 (t) cc_final: 0.7524 (m) REVERT: M 157 LEU cc_start: 0.8342 (mt) cc_final: 0.8046 (pp) REVERT: M 159 THR cc_start: 0.8070 (m) cc_final: 0.7769 (t) REVERT: M 173 LYS cc_start: 0.7756 (tttt) cc_final: 0.7438 (tttt) REVERT: M 183 VAL cc_start: 0.8336 (t) cc_final: 0.8072 (p) REVERT: M 209 CYS cc_start: 0.7552 (t) cc_final: 0.7122 (t) REVERT: M 227 LEU cc_start: 0.8998 (mt) cc_final: 0.8631 (mp) REVERT: M 240 LYS cc_start: 0.8489 (mttt) cc_final: 0.8140 (mttt) REVERT: M 242 TRP cc_start: 0.7155 (t-100) cc_final: 0.6898 (t-100) REVERT: M 257 PHE cc_start: 0.8342 (p90) cc_final: 0.8055 (p90) REVERT: M 258 ARG cc_start: 0.8244 (mtm180) cc_final: 0.7954 (mtm-85) REVERT: M 262 TYR cc_start: 0.8394 (p90) cc_final: 0.7984 (p90) REVERT: M 298 LYS cc_start: 0.8881 (tttt) cc_final: 0.8485 (tttt) REVERT: M 300 ASN cc_start: 0.8910 (p0) cc_final: 0.8653 (p0) REVERT: M 345 LYS cc_start: 0.7245 (ptmm) cc_final: 0.6334 (mtpp) REVERT: M 377 PHE cc_start: 0.7885 (p90) cc_final: 0.7453 (p90) REVERT: M 393 ASP cc_start: 0.7995 (t0) cc_final: 0.7687 (t0) REVERT: M 402 PHE cc_start: 0.7565 (m-80) cc_final: 0.7148 (m-80) REVERT: M 407 TYR cc_start: 0.8578 (m-80) cc_final: 0.8241 (m-80) REVERT: M 414 PHE cc_start: 0.7728 (t80) cc_final: 0.7137 (t80) REVERT: C 21 LEU cc_start: 0.8399 (tp) cc_final: 0.8116 (tp) REVERT: C 51 PHE cc_start: 0.8125 (p90) cc_final: 0.7878 (p90) REVERT: C 53 VAL cc_start: 0.8256 (p) cc_final: 0.8041 (t) REVERT: C 58 TYR cc_start: 0.7903 (t80) cc_final: 0.7374 (t80) REVERT: C 64 THR cc_start: 0.6795 (m) cc_final: 0.6577 (t) REVERT: C 78 TRP cc_start: 0.8170 (m-10) cc_final: 0.7497 (m-10) REVERT: C 81 TYR cc_start: 0.7288 (m-80) cc_final: 0.6757 (m-80) REVERT: C 84 ASN cc_start: 0.8389 (t0) cc_final: 0.7745 (t0) REVERT: C 110 MET cc_start: 0.8384 (mmm) cc_final: 0.7975 (mmm) REVERT: C 128 GLN cc_start: 0.7263 (mm-40) cc_final: 0.6545 (mm-40) REVERT: C 143 LEU cc_start: 0.8857 (mt) cc_final: 0.8642 (mt) REVERT: C 145 LEU cc_start: 0.8231 (mt) cc_final: 0.7972 (mt) REVERT: C 153 TRP cc_start: 0.8508 (p-90) cc_final: 0.7998 (p-90) REVERT: C 159 CYS cc_start: 0.8303 (t) cc_final: 0.7881 (t) REVERT: C 167 TYR cc_start: 0.7850 (m-10) cc_final: 0.7136 (m-80) REVERT: C 168 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7884 (mt-10) REVERT: C 171 ASP cc_start: 0.8327 (m-30) cc_final: 0.7986 (m-30) REVERT: C 172 TRP cc_start: 0.8236 (t60) cc_final: 0.7356 (t60) REVERT: C 176 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7372 (mm-40) REVERT: b 43 LYS cc_start: 0.8186 (mttt) cc_final: 0.7797 (tttp) REVERT: b 50 MET cc_start: 0.8613 (mtm) cc_final: 0.8268 (mpp) REVERT: b 63 MET cc_start: 0.8520 (mmm) cc_final: 0.7749 (mmm) REVERT: b 79 LEU cc_start: 0.8553 (mt) cc_final: 0.8246 (mt) REVERT: b 83 VAL cc_start: 0.8300 (t) cc_final: 0.8012 (t) REVERT: b 85 LYS cc_start: 0.8670 (mttt) cc_final: 0.8463 (mttt) REVERT: b 90 LYS cc_start: 0.8143 (mttm) cc_final: 0.7892 (ttmm) REVERT: b 101 TYR cc_start: 0.8563 (t80) cc_final: 0.8354 (t80) REVERT: b 112 LEU cc_start: 0.8088 (mp) cc_final: 0.7711 (mp) REVERT: b 131 ILE cc_start: 0.8563 (mt) cc_final: 0.8350 (mm) REVERT: b 132 ARG cc_start: 0.8520 (mtt180) cc_final: 0.8202 (ttm170) REVERT: b 139 LEU cc_start: 0.8339 (tp) cc_final: 0.8110 (tt) REVERT: b 141 SER cc_start: 0.8469 (m) cc_final: 0.7945 (t) REVERT: b 142 ILE cc_start: 0.8995 (mm) cc_final: 0.8588 (mp) REVERT: b 151 MET cc_start: 0.7830 (mtp) cc_final: 0.7459 (mtp) REVERT: b 166 VAL cc_start: 0.8695 (t) cc_final: 0.8459 (p) REVERT: b 181 ASP cc_start: 0.8114 (t0) cc_final: 0.7677 (t0) REVERT: b 191 VAL cc_start: 0.8993 (t) cc_final: 0.8736 (p) REVERT: b 195 LEU cc_start: 0.8999 (mt) cc_final: 0.8673 (mt) REVERT: b 196 LEU cc_start: 0.8630 (mt) cc_final: 0.8248 (tp) REVERT: b 202 LEU cc_start: 0.7925 (mm) cc_final: 0.7468 (tt) REVERT: b 207 VAL cc_start: 0.8942 (t) cc_final: 0.8527 (p) REVERT: b 212 GLU cc_start: 0.8333 (tp30) cc_final: 0.8122 (tp30) REVERT: b 215 CYS cc_start: 0.8304 (t) cc_final: 0.8084 (t) REVERT: b 228 LYS cc_start: 0.8531 (ttpt) cc_final: 0.8026 (ttpt) REVERT: b 244 ILE cc_start: 0.9118 (mt) cc_final: 0.8725 (tp) REVERT: b 247 MET cc_start: 0.7626 (tmm) cc_final: 0.6671 (tmm) REVERT: b 298 ARG cc_start: 0.8653 (mmm160) cc_final: 0.7471 (mpt180) REVERT: b 305 LYS cc_start: 0.8737 (tttt) cc_final: 0.8425 (ttpp) REVERT: b 307 LEU cc_start: 0.8922 (mt) cc_final: 0.8667 (mm) REVERT: b 308 LEU cc_start: 0.8636 (mt) cc_final: 0.8307 (mm) REVERT: b 311 ARG cc_start: 0.8387 (ptt180) cc_final: 0.7775 (ptt-90) REVERT: b 317 MET cc_start: 0.8779 (tpp) cc_final: 0.8497 (tpt) REVERT: b 321 GLN cc_start: 0.7916 (tt0) cc_final: 0.7540 (tt0) REVERT: b 322 LEU cc_start: 0.8550 (tt) cc_final: 0.8272 (tt) REVERT: b 326 ILE cc_start: 0.8121 (mm) cc_final: 0.7816 (mm) REVERT: b 341 ARG cc_start: 0.8737 (ptt90) cc_final: 0.7867 (ttp80) REVERT: b 352 ILE cc_start: 0.8613 (mm) cc_final: 0.8397 (mm) REVERT: b 417 ASP cc_start: 0.7771 (t0) cc_final: 0.7342 (t0) REVERT: b 645 ASP cc_start: 0.7838 (t0) cc_final: 0.7119 (p0) REVERT: m 1 MET cc_start: 0.6913 (mtt) cc_final: 0.6350 (mtt) REVERT: m 14 ILE cc_start: 0.8019 (mt) cc_final: 0.7727 (mt) REVERT: m 17 GLU cc_start: 0.7718 (pt0) cc_final: 0.7494 (pt0) REVERT: m 24 VAL cc_start: 0.8609 (t) cc_final: 0.8312 (p) REVERT: m 29 CYS cc_start: 0.8490 (m) cc_final: 0.7937 (t) REVERT: m 33 PHE cc_start: 0.8652 (m-80) cc_final: 0.8230 (m-80) REVERT: m 36 GLN cc_start: 0.8502 (tp40) cc_final: 0.8085 (tp40) REVERT: m 43 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7343 (mt-10) REVERT: m 53 HIS cc_start: 0.8228 (m-70) cc_final: 0.7801 (m170) REVERT: m 60 TYR cc_start: 0.7991 (t80) cc_final: 0.7748 (t80) REVERT: m 64 LEU cc_start: 0.8358 (tp) cc_final: 0.8143 (tp) REVERT: m 71 GLN cc_start: 0.8395 (tp40) cc_final: 0.7721 (tp40) REVERT: m 78 PHE cc_start: 0.8840 (t80) cc_final: 0.8537 (t80) REVERT: m 81 GLU cc_start: 0.7622 (tp30) cc_final: 0.7285 (tp30) REVERT: m 88 ASP cc_start: 0.8593 (m-30) cc_final: 0.8317 (m-30) REVERT: m 89 THR cc_start: 0.8961 (m) cc_final: 0.8739 (m) REVERT: m 92 ASP cc_start: 0.7580 (t70) cc_final: 0.7253 (t70) REVERT: m 103 LYS cc_start: 0.7457 (mtmm) cc_final: 0.7177 (mtmm) REVERT: m 108 ILE cc_start: 0.8800 (mt) cc_final: 0.8398 (mm) REVERT: m 116 MET cc_start: 0.7604 (mtm) cc_final: 0.7011 (mtm) REVERT: m 125 THR cc_start: 0.8546 (m) cc_final: 0.8204 (t) REVERT: m 126 GLU cc_start: 0.8161 (tp30) cc_final: 0.7599 (tp30) REVERT: m 128 ASN cc_start: 0.8626 (m-40) cc_final: 0.7750 (m-40) REVERT: m 134 ILE cc_start: 0.8239 (mt) cc_final: 0.7612 (tp) REVERT: m 140 LEU cc_start: 0.8514 (mt) cc_final: 0.8254 (tt) REVERT: m 141 ARG cc_start: 0.8241 (mmt90) cc_final: 0.7848 (mmt90) REVERT: m 183 VAL cc_start: 0.8327 (t) cc_final: 0.8084 (p) REVERT: m 209 CYS cc_start: 0.7384 (t) cc_final: 0.6317 (m) REVERT: m 220 LEU cc_start: 0.8287 (mm) cc_final: 0.7855 (mm) REVERT: m 234 HIS cc_start: 0.7783 (t-90) cc_final: 0.7336 (t-90) REVERT: m 240 LYS cc_start: 0.8619 (mttt) cc_final: 0.7975 (mmmm) REVERT: m 257 PHE cc_start: 0.8365 (p90) cc_final: 0.8029 (p90) REVERT: m 258 ARG cc_start: 0.8265 (mtm180) cc_final: 0.7994 (mtm-85) REVERT: m 272 ILE cc_start: 0.7565 (mm) cc_final: 0.6868 (mm) REVERT: m 274 VAL cc_start: 0.7952 (t) cc_final: 0.7675 (p) REVERT: m 298 LYS cc_start: 0.8964 (tttt) cc_final: 0.8588 (tttt) REVERT: m 300 ASN cc_start: 0.8992 (p0) cc_final: 0.8764 (p0) REVERT: m 377 PHE cc_start: 0.7749 (p90) cc_final: 0.7390 (p90) REVERT: m 402 PHE cc_start: 0.7584 (m-80) cc_final: 0.6980 (m-80) REVERT: m 414 PHE cc_start: 0.7893 (t80) cc_final: 0.7216 (t80) REVERT: c 18 MET cc_start: 0.6179 (mmt) cc_final: 0.5856 (mmt) REVERT: c 21 LEU cc_start: 0.8444 (tp) cc_final: 0.8213 (tp) REVERT: c 45 THR cc_start: 0.9007 (p) cc_final: 0.8624 (t) REVERT: c 58 TYR cc_start: 0.7931 (t80) cc_final: 0.7189 (t80) REVERT: c 64 THR cc_start: 0.6839 (m) cc_final: 0.6424 (t) REVERT: c 78 TRP cc_start: 0.8199 (m-10) cc_final: 0.7397 (m-10) REVERT: c 84 ASN cc_start: 0.8016 (t0) cc_final: 0.7158 (t0) REVERT: c 86 GLN cc_start: 0.7763 (mm-40) cc_final: 0.6965 (mt0) REVERT: c 110 MET cc_start: 0.8319 (mmm) cc_final: 0.7810 (mmm) REVERT: c 128 GLN cc_start: 0.7438 (mm-40) cc_final: 0.6505 (mm-40) REVERT: c 151 ARG cc_start: 0.8285 (ttm-80) cc_final: 0.8057 (ttm-80) REVERT: c 159 CYS cc_start: 0.8380 (t) cc_final: 0.8032 (t) REVERT: c 167 TYR cc_start: 0.7892 (m-10) cc_final: 0.7236 (m-80) REVERT: c 168 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8005 (mt-10) REVERT: c 171 ASP cc_start: 0.8452 (m-30) cc_final: 0.8147 (m-30) outliers start: 3 outliers final: 2 residues processed: 805 average time/residue: 0.3011 time to fit residues: 343.6507 Evaluate side-chains 754 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 752 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 178 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 376 GLN b 355 GLN ** m 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 54 HIS ** m 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 95 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.134713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.110458 restraints weight = 30968.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.114684 restraints weight = 16780.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.117497 restraints weight = 10498.967| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16108 Z= 0.261 Angle : 0.687 8.758 21822 Z= 0.373 Chirality : 0.048 0.200 2524 Planarity : 0.005 0.041 2752 Dihedral : 11.166 178.519 2154 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.11 % Allowed : 2.55 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.19), residues: 1954 helix: 0.82 (0.18), residues: 820 sheet: -0.00 (0.27), residues: 370 loop : 0.92 (0.25), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP c 66 HIS 0.008 0.001 HIS B 624 PHE 0.024 0.002 PHE C 82 TYR 0.024 0.003 TYR C 58 ARG 0.007 0.001 ARG b 65 Details of bonding type rmsd hydrogen bonds : bond 0.05489 ( 815) hydrogen bonds : angle 5.82917 ( 2361) covalent geometry : bond 0.00495 (16108) covalent geometry : angle 0.68742 (21822) *********************** 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 790 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 788 time to evaluate : 1.662 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: B 43 LYS cc_start: 0.8200 (mttt) cc_final: 0.7718 (tttp) REVERT: B 47 LEU cc_start: 0.9000 (mt) cc_final: 0.8444 (mt) REVERT: B 50 MET cc_start: 0.8650 (mtm) cc_final: 0.8262 (mtm) REVERT: B 51 LEU cc_start: 0.8792 (mt) cc_final: 0.8546 (mt) REVERT: B 52 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7655 (mm-30) REVERT: B 55 LYS cc_start: 0.8471 (ttpt) cc_final: 0.8237 (mtpt) REVERT: B 63 MET cc_start: 0.8510 (mmm) cc_final: 0.7804 (mmm) REVERT: B 66 ILE cc_start: 0.8711 (mm) cc_final: 0.8194 (mm) REVERT: B 72 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8491 (mtpt) REVERT: B 74 LYS cc_start: 0.8796 (mmtt) cc_final: 0.8396 (mmtt) REVERT: B 80 PHE cc_start: 0.8566 (t80) cc_final: 0.7647 (t80) REVERT: B 84 VAL cc_start: 0.8601 (p) cc_final: 0.8304 (m) REVERT: B 85 LYS cc_start: 0.8591 (mttt) cc_final: 0.8224 (mttt) REVERT: B 90 LYS cc_start: 0.8609 (mttt) cc_final: 0.8355 (mttt) REVERT: B 94 ILE cc_start: 0.8442 (mt) cc_final: 0.8138 (mm) REVERT: B 101 TYR cc_start: 0.8636 (t80) cc_final: 0.8414 (t80) REVERT: B 104 ARG cc_start: 0.8739 (tpt90) cc_final: 0.8498 (tpt90) REVERT: B 107 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7469 (mt-10) REVERT: B 112 LEU cc_start: 0.8358 (mp) cc_final: 0.7602 (mp) REVERT: B 121 GLN cc_start: 0.8504 (tt0) cc_final: 0.8297 (tt0) REVERT: B 125 LYS cc_start: 0.8872 (mttt) cc_final: 0.8363 (mtpp) REVERT: B 128 ASN cc_start: 0.8460 (t0) cc_final: 0.8053 (t0) REVERT: B 132 ARG cc_start: 0.8390 (mtt180) cc_final: 0.8112 (ttm110) REVERT: B 137 ARG cc_start: 0.7881 (mtp-110) cc_final: 0.7599 (mtp-110) REVERT: B 151 MET cc_start: 0.7852 (mtp) cc_final: 0.7393 (mtp) REVERT: B 152 MET cc_start: 0.8184 (tpt) cc_final: 0.7930 (tpt) REVERT: B 169 ASN cc_start: 0.8789 (m-40) cc_final: 0.8539 (m-40) REVERT: B 172 HIS cc_start: 0.8602 (m170) cc_final: 0.8132 (m-70) REVERT: B 175 GLN cc_start: 0.8546 (tm-30) cc_final: 0.8154 (tm-30) REVERT: B 177 LEU cc_start: 0.8602 (tp) cc_final: 0.8357 (tp) REVERT: B 183 GLU cc_start: 0.8554 (mp0) cc_final: 0.8222 (mp0) REVERT: B 193 GLU cc_start: 0.8409 (tt0) cc_final: 0.8165 (tt0) REVERT: B 196 LEU cc_start: 0.8683 (mt) cc_final: 0.8343 (tp) REVERT: B 199 LYS cc_start: 0.8110 (mptt) cc_final: 0.7806 (mmtm) REVERT: B 202 LEU cc_start: 0.7903 (mm) cc_final: 0.7497 (tp) REVERT: B 207 VAL cc_start: 0.9012 (t) cc_final: 0.8742 (p) REVERT: B 212 GLU cc_start: 0.8295 (tp30) cc_final: 0.8011 (tp30) REVERT: B 213 GLU cc_start: 0.8281 (tt0) cc_final: 0.7754 (tt0) REVERT: B 215 CYS cc_start: 0.8353 (t) cc_final: 0.7936 (t) REVERT: B 218 ARG cc_start: 0.8953 (mmm160) cc_final: 0.8626 (mtp-110) REVERT: B 228 LYS cc_start: 0.8599 (ttpt) cc_final: 0.8052 (ttpt) REVERT: B 244 ILE cc_start: 0.9122 (mt) cc_final: 0.8679 (tp) REVERT: B 246 HIS cc_start: 0.8504 (m-70) cc_final: 0.8192 (m-70) REVERT: B 247 MET cc_start: 0.7212 (tmm) cc_final: 0.6119 (tmm) REVERT: B 298 ARG cc_start: 0.8627 (mmm160) cc_final: 0.7759 (mpt180) REVERT: B 305 LYS cc_start: 0.8788 (tttt) cc_final: 0.8315 (ttpp) REVERT: B 308 LEU cc_start: 0.8614 (mt) cc_final: 0.8322 (mm) REVERT: B 311 ARG cc_start: 0.8306 (ptt180) cc_final: 0.7614 (ptt-90) REVERT: B 317 MET cc_start: 0.8664 (tpp) cc_final: 0.8284 (tpp) REVERT: B 321 GLN cc_start: 0.8025 (tt0) cc_final: 0.7467 (tt0) REVERT: B 326 ILE cc_start: 0.8104 (mm) cc_final: 0.7806 (mm) REVERT: B 341 ARG cc_start: 0.8823 (ptt90) cc_final: 0.8367 (ptm-80) REVERT: B 346 ASN cc_start: 0.7155 (p0) cc_final: 0.6903 (p0) REVERT: B 351 TYR cc_start: 0.8119 (t80) cc_final: 0.7878 (t80) REVERT: B 388 LEU cc_start: 0.8765 (mt) cc_final: 0.8351 (mm) REVERT: B 391 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7198 (mt-10) REVERT: B 417 ASP cc_start: 0.8166 (t0) cc_final: 0.7912 (t0) REVERT: B 635 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7589 (mt-10) REVERT: B 640 PRO cc_start: 0.8943 (Cg_exo) cc_final: 0.8699 (Cg_endo) REVERT: M 17 GLU cc_start: 0.7752 (pt0) cc_final: 0.7543 (pt0) REVERT: M 21 LYS cc_start: 0.8074 (mttt) cc_final: 0.7387 (mttp) REVERT: M 29 CYS cc_start: 0.8678 (t) cc_final: 0.8273 (t) REVERT: M 30 ASP cc_start: 0.8242 (m-30) cc_final: 0.8023 (t0) REVERT: M 43 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7466 (mt-10) REVERT: M 56 LEU cc_start: 0.8497 (mm) cc_final: 0.8265 (mm) REVERT: M 74 VAL cc_start: 0.8963 (t) cc_final: 0.8674 (p) REVERT: M 78 PHE cc_start: 0.8930 (t80) cc_final: 0.8658 (t80) REVERT: M 88 ASP cc_start: 0.8644 (m-30) cc_final: 0.8312 (m-30) REVERT: M 89 THR cc_start: 0.9004 (m) cc_final: 0.8697 (p) REVERT: M 111 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7911 (mt-10) REVERT: M 114 GLU cc_start: 0.7959 (tp30) cc_final: 0.7332 (tp30) REVERT: M 119 ASN cc_start: 0.8284 (t0) cc_final: 0.7679 (t0) REVERT: M 126 GLU cc_start: 0.8131 (tp30) cc_final: 0.7586 (tp30) REVERT: M 128 ASN cc_start: 0.8283 (m-40) cc_final: 0.7878 (m-40) REVERT: M 131 LYS cc_start: 0.8447 (mtmm) cc_final: 0.8209 (mttp) REVERT: M 135 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8385 (mmtt) REVERT: M 157 LEU cc_start: 0.8496 (mt) cc_final: 0.8243 (pp) REVERT: M 159 THR cc_start: 0.8259 (m) cc_final: 0.7851 (t) REVERT: M 161 GLN cc_start: 0.8349 (tp40) cc_final: 0.8115 (tp-100) REVERT: M 173 LYS cc_start: 0.8209 (tttt) cc_final: 0.7858 (tttt) REVERT: M 183 VAL cc_start: 0.8526 (t) cc_final: 0.8271 (p) REVERT: M 203 GLN cc_start: 0.7145 (mm-40) cc_final: 0.6772 (mm-40) REVERT: M 220 LEU cc_start: 0.8381 (mm) cc_final: 0.8055 (mm) REVERT: M 227 LEU cc_start: 0.8960 (mt) cc_final: 0.8492 (mp) REVERT: M 234 HIS cc_start: 0.8015 (t-90) cc_final: 0.7725 (t-90) REVERT: M 240 LYS cc_start: 0.8517 (mttt) cc_final: 0.7987 (mttt) REVERT: M 242 TRP cc_start: 0.7536 (t-100) cc_final: 0.7086 (t-100) REVERT: M 245 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6423 (mm-30) REVERT: M 251 ILE cc_start: 0.8636 (mm) cc_final: 0.8420 (mm) REVERT: M 257 PHE cc_start: 0.8413 (p90) cc_final: 0.8048 (p90) REVERT: M 258 ARG cc_start: 0.8316 (mtm180) cc_final: 0.8032 (mtm-85) REVERT: M 298 LYS cc_start: 0.9020 (tttt) cc_final: 0.8542 (tttt) REVERT: M 299 GLN cc_start: 0.8265 (mt0) cc_final: 0.6763 (mt0) REVERT: M 377 PHE cc_start: 0.7976 (p90) cc_final: 0.7542 (p90) REVERT: M 393 ASP cc_start: 0.8117 (t0) cc_final: 0.7674 (t0) REVERT: M 402 PHE cc_start: 0.7789 (m-80) cc_final: 0.7231 (m-10) REVERT: M 414 PHE cc_start: 0.7796 (t80) cc_final: 0.7284 (t80) REVERT: C 18 MET cc_start: 0.6632 (mmm) cc_final: 0.6376 (mmm) REVERT: C 23 VAL cc_start: 0.8802 (m) cc_final: 0.8388 (m) REVERT: C 26 ASP cc_start: 0.7598 (m-30) cc_final: 0.7381 (m-30) REVERT: C 37 LEU cc_start: 0.8935 (mt) cc_final: 0.8730 (mt) REVERT: C 51 PHE cc_start: 0.8001 (p90) cc_final: 0.7781 (p90) REVERT: C 58 TYR cc_start: 0.8123 (t80) cc_final: 0.7746 (t80) REVERT: C 64 THR cc_start: 0.6859 (m) cc_final: 0.6545 (t) REVERT: C 68 VAL cc_start: 0.8358 (t) cc_final: 0.8100 (p) REVERT: C 78 TRP cc_start: 0.8260 (m-10) cc_final: 0.7773 (m-10) REVERT: C 84 ASN cc_start: 0.8468 (t0) cc_final: 0.7755 (t0) REVERT: C 86 GLN cc_start: 0.7918 (mm-40) cc_final: 0.7185 (mt0) REVERT: C 128 GLN cc_start: 0.7163 (mm-40) cc_final: 0.6874 (mm-40) REVERT: C 142 LYS cc_start: 0.8923 (mttm) cc_final: 0.8644 (mttm) REVERT: C 145 LEU cc_start: 0.8300 (mt) cc_final: 0.7976 (mt) REVERT: C 153 TRP cc_start: 0.8627 (p-90) cc_final: 0.8029 (p-90) REVERT: C 167 TYR cc_start: 0.8052 (m-10) cc_final: 0.7325 (m-10) REVERT: C 168 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7814 (mt-10) REVERT: C 171 ASP cc_start: 0.8321 (m-30) cc_final: 0.7976 (m-30) REVERT: b 43 LYS cc_start: 0.8246 (mttt) cc_final: 0.7796 (tttp) REVERT: b 47 LEU cc_start: 0.9038 (mt) cc_final: 0.8653 (mt) REVERT: b 48 LYS cc_start: 0.9141 (ptpp) cc_final: 0.8656 (ptpp) REVERT: b 50 MET cc_start: 0.8624 (mtm) cc_final: 0.8350 (mtm) REVERT: b 51 LEU cc_start: 0.8892 (mt) cc_final: 0.8653 (mt) REVERT: b 54 ASN cc_start: 0.7724 (t0) cc_final: 0.6996 (t0) REVERT: b 55 LYS cc_start: 0.8578 (mtpt) cc_final: 0.8084 (mtpt) REVERT: b 63 MET cc_start: 0.8478 (mmm) cc_final: 0.7608 (mmm) REVERT: b 72 LYS cc_start: 0.8857 (mmtt) cc_final: 0.8350 (mtmt) REVERT: b 74 LYS cc_start: 0.8570 (tppt) cc_final: 0.8146 (tppp) REVERT: b 75 ASN cc_start: 0.8247 (p0) cc_final: 0.7991 (p0) REVERT: b 80 PHE cc_start: 0.8622 (t80) cc_final: 0.8081 (t80) REVERT: b 83 VAL cc_start: 0.8188 (t) cc_final: 0.7925 (t) REVERT: b 85 LYS cc_start: 0.8581 (mttt) cc_final: 0.8278 (mttt) REVERT: b 98 VAL cc_start: 0.8885 (t) cc_final: 0.8408 (t) REVERT: b 101 TYR cc_start: 0.8817 (t80) cc_final: 0.8608 (t80) REVERT: b 107 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7591 (mt-10) REVERT: b 112 LEU cc_start: 0.8194 (mp) cc_final: 0.7426 (mp) REVERT: b 131 ILE cc_start: 0.8600 (mt) cc_final: 0.8384 (mm) REVERT: b 132 ARG cc_start: 0.8509 (mtt180) cc_final: 0.8246 (ttm110) REVERT: b 141 SER cc_start: 0.8619 (m) cc_final: 0.8289 (m) REVERT: b 142 ILE cc_start: 0.9064 (mm) cc_final: 0.8740 (mp) REVERT: b 151 MET cc_start: 0.7678 (mtp) cc_final: 0.7246 (mtp) REVERT: b 152 MET cc_start: 0.8157 (tpt) cc_final: 0.7928 (tpt) REVERT: b 162 LEU cc_start: 0.7811 (mt) cc_final: 0.7020 (tp) REVERT: b 175 GLN cc_start: 0.8676 (tm-30) cc_final: 0.8338 (tm-30) REVERT: b 181 ASP cc_start: 0.8382 (t0) cc_final: 0.8008 (t0) REVERT: b 187 MET cc_start: 0.8305 (mtm) cc_final: 0.7936 (mtm) REVERT: b 190 GLU cc_start: 0.8133 (tt0) cc_final: 0.7906 (tt0) REVERT: b 195 LEU cc_start: 0.9143 (mt) cc_final: 0.8818 (mt) REVERT: b 196 LEU cc_start: 0.8767 (mt) cc_final: 0.8343 (tp) REVERT: b 202 LEU cc_start: 0.7918 (mm) cc_final: 0.7539 (tp) REVERT: b 207 VAL cc_start: 0.8945 (t) cc_final: 0.8564 (p) REVERT: b 209 MET cc_start: 0.7542 (tmm) cc_final: 0.7337 (tmm) REVERT: b 212 GLU cc_start: 0.8284 (tp30) cc_final: 0.8010 (tp30) REVERT: b 213 GLU cc_start: 0.8371 (tt0) cc_final: 0.7717 (tt0) REVERT: b 215 CYS cc_start: 0.8360 (t) cc_final: 0.7900 (t) REVERT: b 219 ILE cc_start: 0.9171 (pt) cc_final: 0.8960 (pt) REVERT: b 228 LYS cc_start: 0.8645 (ttpt) cc_final: 0.8184 (ttpt) REVERT: b 244 ILE cc_start: 0.9148 (mt) cc_final: 0.8740 (tp) REVERT: b 246 HIS cc_start: 0.8505 (m-70) cc_final: 0.8177 (m-70) REVERT: b 247 MET cc_start: 0.7452 (tmm) cc_final: 0.6914 (tmm) REVERT: b 298 ARG cc_start: 0.8829 (mmm160) cc_final: 0.7395 (mpt180) REVERT: b 305 LYS cc_start: 0.8759 (tttt) cc_final: 0.8535 (tttm) REVERT: b 307 LEU cc_start: 0.8982 (mt) cc_final: 0.8627 (mt) REVERT: b 308 LEU cc_start: 0.8768 (mt) cc_final: 0.8398 (mm) REVERT: b 311 ARG cc_start: 0.8315 (ptt180) cc_final: 0.7664 (ptt-90) REVERT: b 317 MET cc_start: 0.8716 (tpp) cc_final: 0.8312 (tpp) REVERT: b 321 GLN cc_start: 0.8014 (tt0) cc_final: 0.7581 (tt0) REVERT: b 355 GLN cc_start: 0.8552 (mt0) cc_final: 0.8345 (mt0) REVERT: b 385 ILE cc_start: 0.8702 (mm) cc_final: 0.8496 (mm) REVERT: b 386 LYS cc_start: 0.8740 (mtpt) cc_final: 0.8525 (mtpt) REVERT: b 417 ASP cc_start: 0.7916 (t0) cc_final: 0.7360 (t0) REVERT: b 640 PRO cc_start: 0.8662 (Cg_exo) cc_final: 0.8425 (Cg_endo) REVERT: b 645 ASP cc_start: 0.7848 (t0) cc_final: 0.7265 (p0) REVERT: m 1 MET cc_start: 0.6981 (mtt) cc_final: 0.6491 (mtt) REVERT: m 14 ILE cc_start: 0.8159 (mt) cc_final: 0.7943 (tt) REVERT: m 17 GLU cc_start: 0.7670 (pt0) cc_final: 0.7360 (pt0) REVERT: m 21 LYS cc_start: 0.8080 (mttt) cc_final: 0.7461 (mttm) REVERT: m 29 CYS cc_start: 0.8452 (m) cc_final: 0.8029 (t) REVERT: m 36 GLN cc_start: 0.8469 (tp40) cc_final: 0.8070 (tp40) REVERT: m 43 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7551 (mt-10) REVERT: m 45 VAL cc_start: 0.8926 (t) cc_final: 0.8665 (t) REVERT: m 49 ILE cc_start: 0.8420 (mt) cc_final: 0.8215 (mp) REVERT: m 53 HIS cc_start: 0.8146 (m-70) cc_final: 0.7944 (m-70) REVERT: m 71 GLN cc_start: 0.8420 (tp40) cc_final: 0.7721 (tp40) REVERT: m 74 VAL cc_start: 0.9064 (t) cc_final: 0.8725 (p) REVERT: m 77 LEU cc_start: 0.8669 (mt) cc_final: 0.8417 (mt) REVERT: m 78 PHE cc_start: 0.8865 (t80) cc_final: 0.8425 (t80) REVERT: m 80 ILE cc_start: 0.8604 (mt) cc_final: 0.8317 (mm) REVERT: m 81 GLU cc_start: 0.7786 (tp30) cc_final: 0.7408 (tp30) REVERT: m 88 ASP cc_start: 0.8475 (m-30) cc_final: 0.8253 (m-30) REVERT: m 103 LYS cc_start: 0.7468 (mtmm) cc_final: 0.7173 (mtmm) REVERT: m 111 GLU cc_start: 0.8023 (tt0) cc_final: 0.7650 (tt0) REVERT: m 115 GLU cc_start: 0.8545 (tp30) cc_final: 0.7906 (tp30) REVERT: m 116 MET cc_start: 0.7794 (mtm) cc_final: 0.7527 (mtm) REVERT: m 126 GLU cc_start: 0.8260 (tp30) cc_final: 0.7611 (tp30) REVERT: m 128 ASN cc_start: 0.8349 (m-40) cc_final: 0.7649 (m-40) REVERT: m 134 ILE cc_start: 0.8336 (mt) cc_final: 0.7721 (tp) REVERT: m 140 LEU cc_start: 0.8551 (mt) cc_final: 0.8341 (tt) REVERT: m 141 ARG cc_start: 0.8196 (mmt90) cc_final: 0.7751 (mmt90) REVERT: m 157 LEU cc_start: 0.8495 (mt) cc_final: 0.8205 (pp) REVERT: m 161 GLN cc_start: 0.8396 (tp40) cc_final: 0.8116 (tp-100) REVERT: m 164 ASN cc_start: 0.8924 (p0) cc_final: 0.8694 (p0) REVERT: m 220 LEU cc_start: 0.8293 (mm) cc_final: 0.7985 (mm) REVERT: m 234 HIS cc_start: 0.8192 (t-90) cc_final: 0.7957 (t-90) REVERT: m 240 LYS cc_start: 0.8665 (mttt) cc_final: 0.8059 (mmmm) REVERT: m 242 TRP cc_start: 0.7730 (t-100) cc_final: 0.7337 (t-100) REVERT: m 243 GLU cc_start: 0.8579 (tp30) cc_final: 0.8132 (tp30) REVERT: m 257 PHE cc_start: 0.8477 (p90) cc_final: 0.8143 (p90) REVERT: m 258 ARG cc_start: 0.8386 (mtm180) cc_final: 0.7954 (mtm180) REVERT: m 298 LYS cc_start: 0.9063 (tttt) cc_final: 0.8624 (tttt) REVERT: m 299 GLN cc_start: 0.8437 (mt0) cc_final: 0.6928 (mt0) REVERT: m 378 LYS cc_start: 0.8005 (pttt) cc_final: 0.7617 (ptmm) REVERT: m 400 LYS cc_start: 0.8887 (mmtm) cc_final: 0.8664 (mmtt) REVERT: m 402 PHE cc_start: 0.7553 (m-80) cc_final: 0.7094 (m-80) REVERT: m 406 LYS cc_start: 0.8674 (ttmt) cc_final: 0.8359 (ttmt) REVERT: m 414 PHE cc_start: 0.7905 (t80) cc_final: 0.7610 (t80) REVERT: c 18 MET cc_start: 0.6511 (mmt) cc_final: 0.6121 (mmt) REVERT: c 39 LEU cc_start: 0.8430 (mt) cc_final: 0.8217 (mt) REVERT: c 58 TYR cc_start: 0.8197 (t80) cc_final: 0.7639 (t80) REVERT: c 64 THR cc_start: 0.6870 (m) cc_final: 0.6339 (t) REVERT: c 68 VAL cc_start: 0.8414 (t) cc_final: 0.8208 (p) REVERT: c 78 TRP cc_start: 0.8356 (m-10) cc_final: 0.7801 (m-10) REVERT: c 84 ASN cc_start: 0.8366 (t0) cc_final: 0.7747 (t0) REVERT: c 110 MET cc_start: 0.8542 (mmm) cc_final: 0.8021 (mmm) REVERT: c 115 GLU cc_start: 0.7823 (tt0) cc_final: 0.7543 (tt0) REVERT: c 145 LEU cc_start: 0.8413 (mt) cc_final: 0.8042 (mt) REVERT: c 152 ASN cc_start: 0.8239 (t0) cc_final: 0.7545 (t0) REVERT: c 153 TRP cc_start: 0.8721 (p-90) cc_final: 0.8313 (p-90) REVERT: c 159 CYS cc_start: 0.8422 (t) cc_final: 0.8139 (t) REVERT: c 167 TYR cc_start: 0.8112 (m-10) cc_final: 0.7406 (m-10) REVERT: c 168 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7769 (mt-10) REVERT: c 171 ASP cc_start: 0.8459 (m-30) cc_final: 0.8055 (m-30) REVERT: c 178 ARG cc_start: 0.7983 (ttm170) cc_final: 0.7766 (ttm170) outliers start: 2 outliers final: 0 residues processed: 788 average time/residue: 0.3065 time to fit residues: 340.5254 Evaluate side-chains 751 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 751 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 83 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 60 optimal weight: 0.0870 chunk 15 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 78 optimal weight: 0.0870 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- 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 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 255 GLN b 355 GLN m 26 GLN m 36 GLN m 54 HIS ** m 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 95 ASN y 411 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.139299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.115391 restraints weight = 30759.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.119587 restraints weight = 16735.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.122491 restraints weight = 10444.611| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16108 Z= 0.142 Angle : 0.582 6.709 21822 Z= 0.309 Chirality : 0.046 0.190 2524 Planarity : 0.004 0.048 2752 Dihedral : 10.678 175.394 2154 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.06 % Allowed : 1.59 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.20), residues: 1954 helix: 1.08 (0.18), residues: 816 sheet: 0.10 (0.27), residues: 370 loop : 0.98 (0.25), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 66 HIS 0.003 0.001 HIS b 624 PHE 0.023 0.002 PHE m 121 TYR 0.025 0.002 TYR b 351 ARG 0.005 0.000 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.04463 ( 815) hydrogen bonds : angle 5.36403 ( 2361) covalent geometry : bond 0.00284 (16108) covalent geometry : angle 0.58159 (21822) *********************** 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 761 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 760 time to evaluate : 1.624 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: 0.8241 (mttt) cc_final: 0.7589 (mmmt) REVERT: B 47 LEU cc_start: 0.8965 (mt) cc_final: 0.8467 (mt) REVERT: B 50 MET cc_start: 0.8741 (mtm) cc_final: 0.8187 (mtm) REVERT: B 51 LEU cc_start: 0.8752 (mt) cc_final: 0.8461 (mt) REVERT: B 52 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7503 (mm-30) REVERT: B 54 ASN cc_start: 0.7799 (m110) cc_final: 0.7513 (m110) REVERT: B 63 MET cc_start: 0.8487 (mmm) cc_final: 0.7786 (mmm) REVERT: B 66 ILE cc_start: 0.8616 (mm) cc_final: 0.8201 (mm) REVERT: B 72 LYS cc_start: 0.8887 (mmtt) cc_final: 0.8501 (mtpt) REVERT: B 74 LYS cc_start: 0.8766 (mmtt) cc_final: 0.8319 (mmtt) REVERT: B 80 PHE cc_start: 0.8595 (t80) cc_final: 0.7780 (t80) REVERT: B 83 VAL cc_start: 0.8340 (t) cc_final: 0.8096 (t) REVERT: B 84 VAL cc_start: 0.8567 (p) cc_final: 0.8268 (m) REVERT: B 85 LYS cc_start: 0.8595 (mttt) cc_final: 0.8129 (mttt) REVERT: B 90 LYS cc_start: 0.8537 (mttt) cc_final: 0.8247 (mttt) REVERT: B 94 ILE cc_start: 0.8306 (mt) cc_final: 0.8028 (mm) REVERT: B 98 VAL cc_start: 0.8632 (t) cc_final: 0.8201 (t) REVERT: B 107 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7381 (mt-10) REVERT: B 112 LEU cc_start: 0.8336 (mp) cc_final: 0.7609 (mp) REVERT: B 125 LYS cc_start: 0.8887 (mttt) cc_final: 0.8392 (mtpp) REVERT: B 132 ARG cc_start: 0.8299 (mtt180) cc_final: 0.7978 (mtm180) REVERT: B 137 ARG cc_start: 0.7759 (mtp-110) cc_final: 0.7371 (mtp-110) REVERT: B 147 ILE cc_start: 0.8490 (pt) cc_final: 0.7777 (pt) REVERT: B 151 MET cc_start: 0.7804 (mtp) cc_final: 0.7063 (mtp) REVERT: B 152 MET cc_start: 0.8012 (tpt) cc_final: 0.7779 (tpt) REVERT: B 155 ILE cc_start: 0.9238 (mm) cc_final: 0.8995 (mm) REVERT: B 169 ASN cc_start: 0.8656 (m-40) cc_final: 0.8452 (m-40) REVERT: B 175 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8044 (tm-30) REVERT: B 183 GLU cc_start: 0.8571 (mp0) cc_final: 0.8233 (mp0) REVERT: B 190 GLU cc_start: 0.8164 (tt0) cc_final: 0.7949 (tt0) REVERT: B 193 GLU cc_start: 0.8401 (tt0) cc_final: 0.8099 (tt0) REVERT: B 196 LEU cc_start: 0.8789 (mt) cc_final: 0.8393 (tp) REVERT: B 199 LYS cc_start: 0.8006 (mptt) cc_final: 0.7796 (mmtm) REVERT: B 202 LEU cc_start: 0.7684 (mm) cc_final: 0.7230 (tp) REVERT: B 207 VAL cc_start: 0.8793 (t) cc_final: 0.8526 (p) REVERT: B 213 GLU cc_start: 0.8158 (tt0) cc_final: 0.7685 (tt0) REVERT: B 215 CYS cc_start: 0.8306 (t) cc_final: 0.7815 (t) REVERT: B 228 LYS cc_start: 0.8582 (ttpt) cc_final: 0.8029 (ttpt) REVERT: B 244 ILE cc_start: 0.9067 (mt) cc_final: 0.8639 (tp) REVERT: B 246 HIS cc_start: 0.8505 (m-70) cc_final: 0.8242 (m-70) REVERT: B 247 MET cc_start: 0.7200 (tmm) cc_final: 0.6691 (tmm) REVERT: B 298 ARG cc_start: 0.8586 (mmm160) cc_final: 0.7728 (mpt180) REVERT: B 305 LYS cc_start: 0.8752 (tttt) cc_final: 0.8485 (tttp) REVERT: B 308 LEU cc_start: 0.8567 (mt) cc_final: 0.8240 (mm) REVERT: B 317 MET cc_start: 0.8645 (tpp) cc_final: 0.8256 (tpp) REVERT: B 321 GLN cc_start: 0.8029 (tt0) cc_final: 0.7490 (tt0) REVERT: B 341 ARG cc_start: 0.8678 (ptt90) cc_final: 0.8045 (ptm-80) REVERT: B 351 TYR cc_start: 0.7978 (t80) cc_final: 0.7320 (t80) REVERT: B 355 GLN cc_start: 0.8666 (mt0) cc_final: 0.8447 (mt0) REVERT: B 367 MET cc_start: 0.6942 (mtp) cc_final: 0.6458 (mtp) REVERT: B 387 THR cc_start: 0.8362 (m) cc_final: 0.8057 (m) REVERT: B 388 LEU cc_start: 0.8731 (mt) cc_final: 0.8407 (mm) REVERT: B 391 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7164 (mt-10) REVERT: M 1 MET cc_start: 0.7112 (mpp) cc_final: 0.6625 (mpp) REVERT: M 17 GLU cc_start: 0.7567 (pt0) cc_final: 0.7361 (pt0) REVERT: M 21 LYS cc_start: 0.7948 (mttt) cc_final: 0.7105 (mttm) REVERT: M 29 CYS cc_start: 0.8609 (t) cc_final: 0.8229 (t) REVERT: M 30 ASP cc_start: 0.8112 (m-30) cc_final: 0.7901 (t0) REVERT: M 34 GLU cc_start: 0.9006 (tt0) cc_final: 0.8717 (tt0) REVERT: M 43 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7424 (mt-10) REVERT: M 64 LEU cc_start: 0.8584 (tp) cc_final: 0.8347 (tp) REVERT: M 85 ARG cc_start: 0.8921 (tpp80) cc_final: 0.8709 (tpp80) REVERT: M 88 ASP cc_start: 0.8566 (m-30) cc_final: 0.8328 (m-30) REVERT: M 89 THR cc_start: 0.9017 (m) cc_final: 0.8671 (p) REVERT: M 92 ASP cc_start: 0.7886 (t70) cc_final: 0.7666 (t0) REVERT: M 116 MET cc_start: 0.7881 (mtm) cc_final: 0.7429 (mtm) REVERT: M 119 ASN cc_start: 0.8200 (t0) cc_final: 0.7581 (t0) REVERT: M 126 GLU cc_start: 0.8173 (tp30) cc_final: 0.7729 (tp30) REVERT: M 128 ASN cc_start: 0.8322 (m-40) cc_final: 0.8043 (m110) REVERT: M 131 LYS cc_start: 0.8530 (mtmm) cc_final: 0.8003 (mttp) REVERT: M 134 ILE cc_start: 0.8425 (mt) cc_final: 0.8198 (mt) REVERT: M 135 LYS cc_start: 0.8895 (mmtt) cc_final: 0.8418 (mmtt) REVERT: M 157 LEU cc_start: 0.8512 (mt) cc_final: 0.8246 (pp) REVERT: M 159 THR cc_start: 0.8235 (m) cc_final: 0.7840 (t) REVERT: M 161 GLN cc_start: 0.8321 (tp40) cc_final: 0.8064 (tp-100) REVERT: M 203 GLN cc_start: 0.7260 (mm-40) cc_final: 0.6978 (mm-40) REVERT: M 209 CYS cc_start: 0.7351 (t) cc_final: 0.6522 (m) REVERT: M 220 LEU cc_start: 0.8237 (mm) cc_final: 0.7813 (mm) REVERT: M 227 LEU cc_start: 0.8918 (mt) cc_final: 0.8562 (mp) REVERT: M 242 TRP cc_start: 0.7571 (t-100) cc_final: 0.7185 (t-100) REVERT: M 245 GLU cc_start: 0.6814 (mm-30) cc_final: 0.6302 (mm-30) REVERT: M 257 PHE cc_start: 0.8426 (p90) cc_final: 0.8106 (p90) REVERT: M 258 ARG cc_start: 0.8341 (mtm180) cc_final: 0.8061 (mtm-85) REVERT: M 262 TYR cc_start: 0.8391 (p90) cc_final: 0.8029 (p90) REVERT: M 298 LYS cc_start: 0.9044 (tttt) cc_final: 0.8658 (tttt) REVERT: M 300 ASN cc_start: 0.9101 (p0) cc_final: 0.8860 (p0) REVERT: M 377 PHE cc_start: 0.7899 (p90) cc_final: 0.7455 (p90) REVERT: M 393 ASP cc_start: 0.8006 (t0) cc_final: 0.7545 (t0) REVERT: M 402 PHE cc_start: 0.7720 (m-80) cc_final: 0.7179 (m-80) REVERT: M 414 PHE cc_start: 0.7821 (t80) cc_final: 0.7272 (t80) REVERT: C 18 MET cc_start: 0.6488 (mmm) cc_final: 0.6132 (mmm) REVERT: C 23 VAL cc_start: 0.8717 (m) cc_final: 0.8313 (m) REVERT: C 44 THR cc_start: 0.9149 (m) cc_final: 0.8764 (p) REVERT: C 57 GLU cc_start: 0.7824 (tt0) cc_final: 0.7593 (tt0) REVERT: C 64 THR cc_start: 0.6748 (m) cc_final: 0.6464 (t) REVERT: C 68 VAL cc_start: 0.8302 (t) cc_final: 0.8029 (p) REVERT: C 78 TRP cc_start: 0.8290 (m-10) cc_final: 0.7949 (m-10) REVERT: C 82 PHE cc_start: 0.8226 (m-80) cc_final: 0.8009 (m-80) REVERT: C 84 ASN cc_start: 0.8460 (t0) cc_final: 0.7704 (t0) REVERT: C 86 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7306 (mt0) REVERT: C 95 ASN cc_start: 0.7716 (t0) cc_final: 0.7487 (t0) REVERT: C 142 LYS cc_start: 0.8941 (mttm) cc_final: 0.8661 (mttm) REVERT: C 145 LEU cc_start: 0.8212 (mt) cc_final: 0.7868 (mt) REVERT: C 151 ARG cc_start: 0.8720 (tpp-160) cc_final: 0.8434 (tpt170) REVERT: C 153 TRP cc_start: 0.8584 (p-90) cc_final: 0.8114 (p-90) REVERT: C 168 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7593 (mt-10) REVERT: C 171 ASP cc_start: 0.8184 (m-30) cc_final: 0.7789 (m-30) REVERT: C 178 ARG cc_start: 0.7866 (ttm170) cc_final: 0.7666 (ttm170) REVERT: b 43 LYS cc_start: 0.8269 (mttt) cc_final: 0.7738 (tttp) REVERT: b 47 LEU cc_start: 0.9024 (mt) cc_final: 0.8704 (mt) REVERT: b 63 MET cc_start: 0.8390 (mmm) cc_final: 0.8005 (mmm) REVERT: b 66 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8101 (mp) REVERT: b 72 LYS cc_start: 0.8782 (mmtt) cc_final: 0.8256 (mtmt) REVERT: b 80 PHE cc_start: 0.8519 (t80) cc_final: 0.7887 (t80) REVERT: b 83 VAL cc_start: 0.8091 (t) cc_final: 0.7825 (t) REVERT: b 85 LYS cc_start: 0.8599 (mttt) cc_final: 0.8124 (mttt) REVERT: b 107 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7475 (mt-10) REVERT: b 131 ILE cc_start: 0.8525 (mt) cc_final: 0.8319 (mm) REVERT: b 132 ARG cc_start: 0.8430 (mtt180) cc_final: 0.8151 (mtm180) REVERT: b 141 SER cc_start: 0.8560 (m) cc_final: 0.8271 (m) REVERT: b 142 ILE cc_start: 0.9067 (mm) cc_final: 0.8751 (mp) REVERT: b 151 MET cc_start: 0.7604 (mtp) cc_final: 0.7162 (mtp) REVERT: b 152 MET cc_start: 0.8038 (tpt) cc_final: 0.7824 (tpt) REVERT: b 155 ILE cc_start: 0.9260 (mm) cc_final: 0.9053 (mm) REVERT: b 162 LEU cc_start: 0.7803 (mt) cc_final: 0.6985 (tp) REVERT: b 175 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8243 (tm-30) REVERT: b 181 ASP cc_start: 0.8325 (t0) cc_final: 0.7916 (t0) REVERT: b 187 MET cc_start: 0.8206 (mtm) cc_final: 0.7645 (mtm) REVERT: b 195 LEU cc_start: 0.9058 (mt) cc_final: 0.8728 (mt) REVERT: b 196 LEU cc_start: 0.8833 (mt) cc_final: 0.8482 (tp) REVERT: b 199 LYS cc_start: 0.8246 (mppt) cc_final: 0.7949 (mmtm) REVERT: b 202 LEU cc_start: 0.7702 (mm) cc_final: 0.7277 (tp) REVERT: b 207 VAL cc_start: 0.8874 (t) cc_final: 0.8458 (p) REVERT: b 212 GLU cc_start: 0.7915 (tp30) cc_final: 0.7593 (tp30) REVERT: b 213 GLU cc_start: 0.8300 (tt0) cc_final: 0.7589 (tt0) REVERT: b 215 CYS cc_start: 0.8294 (t) cc_final: 0.7675 (t) REVERT: b 218 ARG cc_start: 0.8925 (mmm160) cc_final: 0.8539 (mtp85) REVERT: b 228 LYS cc_start: 0.8590 (ttpt) cc_final: 0.8161 (ttpt) REVERT: b 244 ILE cc_start: 0.9118 (mt) cc_final: 0.8712 (tp) REVERT: b 246 HIS cc_start: 0.8476 (m-70) cc_final: 0.8215 (m-70) REVERT: b 247 MET cc_start: 0.7350 (tmm) cc_final: 0.5854 (tmm) REVERT: b 298 ARG cc_start: 0.8841 (mmm160) cc_final: 0.8020 (mpt180) REVERT: b 302 ARG cc_start: 0.8821 (ttm-80) cc_final: 0.8286 (mpt180) REVERT: b 307 LEU cc_start: 0.8918 (mt) cc_final: 0.8550 (mt) REVERT: b 308 LEU cc_start: 0.8703 (mt) cc_final: 0.8362 (mm) REVERT: b 311 ARG cc_start: 0.8368 (ptt180) cc_final: 0.7747 (ptt-90) REVERT: b 317 MET cc_start: 0.8639 (tpp) cc_final: 0.8253 (tpp) REVERT: b 321 GLN cc_start: 0.7910 (tt0) cc_final: 0.7379 (tt0) REVERT: b 324 TRP cc_start: 0.8760 (t-100) cc_final: 0.8208 (t-100) REVERT: b 341 ARG cc_start: 0.8679 (ptt90) cc_final: 0.7969 (ttp80) REVERT: b 352 ILE cc_start: 0.8677 (mm) cc_final: 0.8471 (mm) REVERT: b 384 MET cc_start: 0.7965 (ptt) cc_final: 0.7423 (ptt) REVERT: b 386 LYS cc_start: 0.8595 (mtpt) cc_final: 0.8356 (mtpt) REVERT: b 417 ASP cc_start: 0.7965 (t0) cc_final: 0.7201 (t0) REVERT: m 17 GLU cc_start: 0.7518 (pt0) cc_final: 0.7228 (pt0) REVERT: m 21 LYS cc_start: 0.7942 (mttt) cc_final: 0.7420 (mttm) REVERT: m 29 CYS cc_start: 0.8465 (m) cc_final: 0.7897 (t) REVERT: m 36 GLN cc_start: 0.8367 (tp-100) cc_final: 0.7977 (tp-100) REVERT: m 37 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8436 (tm-30) REVERT: m 43 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7439 (mt-10) REVERT: m 44 ASN cc_start: 0.8205 (t0) cc_final: 0.7435 (t0) REVERT: m 45 VAL cc_start: 0.8899 (t) cc_final: 0.8627 (t) REVERT: m 53 HIS cc_start: 0.8067 (m-70) cc_final: 0.7861 (m-70) REVERT: m 71 GLN cc_start: 0.8383 (tp40) cc_final: 0.7913 (tp-100) REVERT: m 74 VAL cc_start: 0.9034 (t) cc_final: 0.8794 (p) REVERT: m 77 LEU cc_start: 0.8544 (mt) cc_final: 0.8281 (mt) REVERT: m 80 ILE cc_start: 0.8507 (mt) cc_final: 0.8197 (mm) REVERT: m 81 GLU cc_start: 0.7759 (tp30) cc_final: 0.7426 (tp30) REVERT: m 88 ASP cc_start: 0.8415 (m-30) cc_final: 0.8191 (m-30) REVERT: m 89 THR cc_start: 0.8982 (m) cc_final: 0.8653 (p) REVERT: m 103 LYS cc_start: 0.7300 (mtmm) cc_final: 0.6987 (mtmm) REVERT: m 111 GLU cc_start: 0.7974 (tt0) cc_final: 0.7620 (tt0) REVERT: m 116 MET cc_start: 0.7715 (mtm) cc_final: 0.7316 (mtm) REVERT: m 123 LEU cc_start: 0.8446 (tp) cc_final: 0.8225 (tp) REVERT: m 126 GLU cc_start: 0.8249 (tp30) cc_final: 0.7512 (tp30) REVERT: m 128 ASN cc_start: 0.8347 (m-40) cc_final: 0.7640 (m-40) REVERT: m 129 ILE cc_start: 0.8909 (mm) cc_final: 0.8616 (tp) REVERT: m 134 ILE cc_start: 0.8292 (mt) cc_final: 0.7758 (tp) REVERT: m 140 LEU cc_start: 0.8455 (mt) cc_final: 0.8235 (tt) REVERT: m 141 ARG cc_start: 0.8125 (mmt90) cc_final: 0.7677 (mmt90) REVERT: m 161 GLN cc_start: 0.8351 (tp40) cc_final: 0.8096 (tp-100) REVERT: m 209 CYS cc_start: 0.7337 (t) cc_final: 0.6461 (m) REVERT: m 220 LEU cc_start: 0.8171 (mm) cc_final: 0.7800 (mm) REVERT: m 234 HIS cc_start: 0.8002 (t-90) cc_final: 0.7715 (t-90) REVERT: m 240 LYS cc_start: 0.8594 (mttt) cc_final: 0.7989 (mmmm) REVERT: m 243 GLU cc_start: 0.8565 (tp30) cc_final: 0.8108 (tp30) REVERT: m 257 PHE cc_start: 0.8516 (p90) cc_final: 0.8222 (p90) REVERT: m 258 ARG cc_start: 0.8382 (mtm180) cc_final: 0.8117 (mtm-85) REVERT: m 262 TYR cc_start: 0.8206 (p90) cc_final: 0.7136 (p90) REVERT: m 298 LYS cc_start: 0.9086 (tttt) cc_final: 0.8690 (tttt) REVERT: m 300 ASN cc_start: 0.9104 (p0) cc_final: 0.8878 (p0) REVERT: m 377 PHE cc_start: 0.7789 (p90) cc_final: 0.7565 (p90) REVERT: m 393 ASP cc_start: 0.8022 (t0) cc_final: 0.7741 (t0) REVERT: m 400 LYS cc_start: 0.8866 (mmtm) cc_final: 0.8603 (mmtt) REVERT: m 402 PHE cc_start: 0.7556 (m-80) cc_final: 0.7226 (m-80) REVERT: m 406 LYS cc_start: 0.8710 (ttmt) cc_final: 0.8428 (ttmt) REVERT: m 407 TYR cc_start: 0.8610 (m-80) cc_final: 0.8060 (m-80) REVERT: m 414 PHE cc_start: 0.7868 (t80) cc_final: 0.7449 (t80) REVERT: c 18 MET cc_start: 0.6393 (mmt) cc_final: 0.6154 (mmt) REVERT: c 30 LYS cc_start: 0.8098 (mtmm) cc_final: 0.7266 (mtmm) REVERT: c 58 TYR cc_start: 0.8177 (t80) cc_final: 0.7589 (t80) REVERT: c 64 THR cc_start: 0.6662 (m) cc_final: 0.6330 (t) REVERT: c 68 VAL cc_start: 0.8386 (t) cc_final: 0.8063 (p) REVERT: c 81 TYR cc_start: 0.7090 (m-80) cc_final: 0.6507 (m-80) REVERT: c 82 PHE cc_start: 0.8174 (m-80) cc_final: 0.7785 (m-80) REVERT: c 84 ASN cc_start: 0.8283 (t0) cc_final: 0.7630 (t0) REVERT: c 110 MET cc_start: 0.8490 (mmm) cc_final: 0.7891 (mmm) REVERT: c 115 GLU cc_start: 0.7782 (tt0) cc_final: 0.7530 (tt0) REVERT: c 134 MET cc_start: 0.7609 (mpp) cc_final: 0.5310 (mpp) REVERT: c 135 ASN cc_start: 0.8178 (p0) cc_final: 0.7548 (p0) REVERT: c 145 LEU cc_start: 0.8274 (mt) cc_final: 0.7872 (mt) REVERT: c 152 ASN cc_start: 0.7811 (t0) cc_final: 0.7352 (t0) REVERT: c 153 TRP cc_start: 0.8684 (p-90) cc_final: 0.8170 (p-90) REVERT: c 167 TYR cc_start: 0.8015 (m-10) cc_final: 0.7219 (m-10) REVERT: c 171 ASP cc_start: 0.8194 (m-30) cc_final: 0.7797 (m-30) REVERT: c 178 ARG cc_start: 0.7946 (ttm170) cc_final: 0.7716 (ttm170) outliers start: 1 outliers final: 0 residues processed: 760 average time/residue: 0.3047 time to fit residues: 326.9744 Evaluate side-chains 731 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 730 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 48 optimal weight: 0.8980 chunk 40 optimal weight: 0.0370 chunk 177 optimal weight: 0.5980 chunk 192 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 138 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 169 optimal weight: 0.7980 chunk 70 optimal weight: 20.0000 chunk 148 optimal weight: 0.0070 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 26 GLN m 390 ASN c 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.140839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.116135 restraints weight = 31025.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.120511 restraints weight = 16712.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.123551 restraints weight = 10462.124| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16108 Z= 0.129 Angle : 0.564 7.054 21822 Z= 0.295 Chirality : 0.044 0.182 2524 Planarity : 0.004 0.042 2752 Dihedral : 10.213 168.979 2154 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.06 % Allowed : 1.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.20), residues: 1954 helix: 1.20 (0.18), residues: 810 sheet: 0.24 (0.27), residues: 374 loop : 0.99 (0.25), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 172 HIS 0.003 0.001 HIS b 223 PHE 0.022 0.001 PHE C 51 TYR 0.027 0.002 TYR M 399 ARG 0.008 0.000 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.04164 ( 815) hydrogen bonds : angle 5.11059 ( 2361) covalent geometry : bond 0.00256 (16108) covalent geometry : angle 0.56419 (21822) *********************** 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 752 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 751 time to evaluate : 1.838 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: 0.8222 (mttt) cc_final: 0.7668 (mmmt) REVERT: B 47 LEU cc_start: 0.8958 (mt) cc_final: 0.8565 (mt) REVERT: B 50 MET cc_start: 0.8679 (mtm) cc_final: 0.8169 (mtm) REVERT: B 51 LEU cc_start: 0.8858 (mt) cc_final: 0.8524 (mt) REVERT: B 52 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7521 (mm-30) REVERT: B 54 ASN cc_start: 0.7904 (m110) cc_final: 0.7599 (m110) REVERT: B 59 LYS cc_start: 0.8609 (mttt) cc_final: 0.8188 (ptpp) REVERT: B 63 MET cc_start: 0.8502 (mmm) cc_final: 0.7956 (mmm) REVERT: B 66 ILE cc_start: 0.8583 (mm) cc_final: 0.8328 (mm) REVERT: B 72 LYS cc_start: 0.8881 (mmtt) cc_final: 0.8419 (mtpt) REVERT: B 74 LYS cc_start: 0.8774 (mmtt) cc_final: 0.8347 (mmtt) REVERT: B 80 PHE cc_start: 0.8612 (t80) cc_final: 0.8002 (t80) REVERT: B 85 LYS cc_start: 0.8610 (mttt) cc_final: 0.7962 (mttt) REVERT: B 90 LYS cc_start: 0.8513 (mttt) cc_final: 0.8222 (mttt) REVERT: B 98 VAL cc_start: 0.8569 (t) cc_final: 0.8368 (t) REVERT: B 112 LEU cc_start: 0.8277 (mp) cc_final: 0.7679 (mp) REVERT: B 121 GLN cc_start: 0.8361 (tt0) cc_final: 0.8140 (tt0) REVERT: B 125 LYS cc_start: 0.8832 (mttt) cc_final: 0.8409 (mtpp) REVERT: B 132 ARG cc_start: 0.8217 (mtt180) cc_final: 0.8004 (mtm180) REVERT: B 137 ARG cc_start: 0.7739 (mtp-110) cc_final: 0.7379 (mtp-110) REVERT: B 147 ILE cc_start: 0.8447 (pt) cc_final: 0.7739 (pt) REVERT: B 151 MET cc_start: 0.7791 (mtp) cc_final: 0.7036 (mtp) REVERT: B 155 ILE cc_start: 0.9208 (mm) cc_final: 0.8904 (mm) REVERT: B 169 ASN cc_start: 0.8630 (m-40) cc_final: 0.8426 (m-40) REVERT: B 175 GLN cc_start: 0.8517 (tm-30) cc_final: 0.8110 (tm-30) REVERT: B 181 ASP cc_start: 0.8453 (t0) cc_final: 0.7974 (t0) REVERT: B 190 GLU cc_start: 0.8120 (tt0) cc_final: 0.7821 (tt0) REVERT: B 193 GLU cc_start: 0.8403 (tt0) cc_final: 0.8125 (tt0) REVERT: B 202 LEU cc_start: 0.7393 (mm) cc_final: 0.6983 (tp) REVERT: B 207 VAL cc_start: 0.8752 (t) cc_final: 0.8466 (p) REVERT: B 213 GLU cc_start: 0.8135 (tt0) cc_final: 0.7681 (tt0) REVERT: B 228 LYS cc_start: 0.8606 (ttpt) cc_final: 0.8063 (ttpt) REVERT: B 241 GLN cc_start: 0.8295 (mt0) cc_final: 0.7551 (mt0) REVERT: B 244 ILE cc_start: 0.9033 (mt) cc_final: 0.8578 (tp) REVERT: B 247 MET cc_start: 0.7311 (tmm) cc_final: 0.6793 (tmm) REVERT: B 298 ARG cc_start: 0.8634 (mmm160) cc_final: 0.7720 (mpt180) REVERT: B 301 ILE cc_start: 0.8735 (mt) cc_final: 0.8453 (mt) REVERT: B 305 LYS cc_start: 0.8685 (tttt) cc_final: 0.8404 (tttm) REVERT: B 308 LEU cc_start: 0.8634 (mt) cc_final: 0.8270 (mm) REVERT: B 311 ARG cc_start: 0.8201 (ptt180) cc_final: 0.7577 (ptt-90) REVERT: B 317 MET cc_start: 0.8601 (tpp) cc_final: 0.8190 (tpp) REVERT: B 321 GLN cc_start: 0.8079 (tt0) cc_final: 0.7590 (tt0) REVERT: B 324 TRP cc_start: 0.8740 (t-100) cc_final: 0.8343 (t-100) REVERT: B 341 ARG cc_start: 0.8676 (ptt90) cc_final: 0.8238 (ptm-80) REVERT: B 360 MET cc_start: 0.8523 (tpp) cc_final: 0.6735 (tpp) REVERT: B 367 MET cc_start: 0.6796 (mtp) cc_final: 0.6543 (mtp) REVERT: B 387 THR cc_start: 0.8324 (m) cc_final: 0.7875 (m) REVERT: B 388 LEU cc_start: 0.8811 (mt) cc_final: 0.8318 (mm) REVERT: B 391 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7029 (mt-10) REVERT: M 1 MET cc_start: 0.6899 (mpp) cc_final: 0.6367 (mpp) REVERT: M 17 GLU cc_start: 0.7650 (pt0) cc_final: 0.7215 (pt0) REVERT: M 21 LYS cc_start: 0.7924 (mttt) cc_final: 0.7165 (mttm) REVERT: M 29 CYS cc_start: 0.8616 (t) cc_final: 0.8228 (t) REVERT: M 31 TYR cc_start: 0.8127 (m-80) cc_final: 0.7898 (m-10) REVERT: M 34 GLU cc_start: 0.9008 (tt0) cc_final: 0.8551 (tt0) REVERT: M 43 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7493 (mt-10) REVERT: M 77 LEU cc_start: 0.8479 (mt) cc_final: 0.8038 (mt) REVERT: M 88 ASP cc_start: 0.8539 (m-30) cc_final: 0.8316 (m-30) REVERT: M 89 THR cc_start: 0.8991 (m) cc_final: 0.8687 (p) REVERT: M 116 MET cc_start: 0.7870 (mtm) cc_final: 0.7481 (mtm) REVERT: M 119 ASN cc_start: 0.8147 (t0) cc_final: 0.7664 (t0) REVERT: M 123 LEU cc_start: 0.8605 (tp) cc_final: 0.8368 (tp) REVERT: M 126 GLU cc_start: 0.8191 (tp30) cc_final: 0.7552 (tp30) REVERT: M 128 ASN cc_start: 0.8343 (m-40) cc_final: 0.8009 (m-40) REVERT: M 131 LYS cc_start: 0.8478 (mtmm) cc_final: 0.7963 (mttp) REVERT: M 134 ILE cc_start: 0.8347 (mt) cc_final: 0.8098 (mt) REVERT: M 135 LYS cc_start: 0.8902 (mmtt) cc_final: 0.8423 (mmtt) REVERT: M 157 LEU cc_start: 0.8363 (mt) cc_final: 0.8014 (pp) REVERT: M 159 THR cc_start: 0.8142 (m) cc_final: 0.7905 (p) REVERT: M 161 GLN cc_start: 0.8355 (tp40) cc_final: 0.8132 (tp-100) REVERT: M 172 VAL cc_start: 0.8833 (t) cc_final: 0.8495 (m) REVERT: M 203 GLN cc_start: 0.7185 (mm-40) cc_final: 0.6896 (mm-40) REVERT: M 209 CYS cc_start: 0.7276 (t) cc_final: 0.6350 (m) REVERT: M 220 LEU cc_start: 0.8197 (mm) cc_final: 0.7771 (mm) REVERT: M 227 LEU cc_start: 0.8982 (mt) cc_final: 0.8603 (mp) REVERT: M 234 HIS cc_start: 0.7935 (t-90) cc_final: 0.7698 (t-90) REVERT: M 242 TRP cc_start: 0.7617 (t-100) cc_final: 0.7239 (t-100) REVERT: M 245 GLU cc_start: 0.6778 (mm-30) cc_final: 0.6243 (mm-30) REVERT: M 257 PHE cc_start: 0.8459 (p90) cc_final: 0.8081 (p90) REVERT: M 258 ARG cc_start: 0.8350 (mtm180) cc_final: 0.7754 (mtm180) REVERT: M 262 TYR cc_start: 0.8390 (p90) cc_final: 0.8067 (p90) REVERT: M 298 LYS cc_start: 0.9006 (tttt) cc_final: 0.8615 (tttt) REVERT: M 300 ASN cc_start: 0.9067 (p0) cc_final: 0.8738 (p0) REVERT: M 377 PHE cc_start: 0.7905 (p90) cc_final: 0.7483 (p90) REVERT: M 393 ASP cc_start: 0.7929 (t0) cc_final: 0.7462 (t0) REVERT: M 402 PHE cc_start: 0.7729 (m-80) cc_final: 0.7196 (m-80) REVERT: M 414 PHE cc_start: 0.7807 (t80) cc_final: 0.7276 (t80) REVERT: C 18 MET cc_start: 0.6484 (mmm) cc_final: 0.6167 (mmm) REVERT: C 23 VAL cc_start: 0.8738 (m) cc_final: 0.8224 (m) REVERT: C 44 THR cc_start: 0.9164 (m) cc_final: 0.8762 (p) REVERT: C 64 THR cc_start: 0.6669 (m) cc_final: 0.6386 (t) REVERT: C 68 VAL cc_start: 0.8195 (t) cc_final: 0.7902 (p) REVERT: C 78 TRP cc_start: 0.8253 (m-10) cc_final: 0.7849 (m-10) REVERT: C 81 TYR cc_start: 0.7177 (m-80) cc_final: 0.6481 (m-80) REVERT: C 84 ASN cc_start: 0.8500 (t0) cc_final: 0.7710 (t0) REVERT: C 86 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7247 (mt0) REVERT: C 95 ASN cc_start: 0.7691 (t0) cc_final: 0.7419 (t0) REVERT: C 110 MET cc_start: 0.8602 (mmm) cc_final: 0.8053 (mmm) REVERT: C 115 GLU cc_start: 0.8024 (tt0) cc_final: 0.7722 (tt0) REVERT: C 116 LEU cc_start: 0.8075 (mt) cc_final: 0.7689 (mt) REVERT: C 142 LYS cc_start: 0.8953 (mttm) cc_final: 0.8698 (mttm) REVERT: C 145 LEU cc_start: 0.8042 (mt) cc_final: 0.7836 (mt) REVERT: C 168 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7597 (mt-10) REVERT: C 171 ASP cc_start: 0.8090 (m-30) cc_final: 0.7750 (m-30) REVERT: C 178 ARG cc_start: 0.7945 (ttm170) cc_final: 0.7704 (ttm170) REVERT: b 43 LYS cc_start: 0.8136 (mttt) cc_final: 0.7722 (tttp) REVERT: b 47 LEU cc_start: 0.8973 (mt) cc_final: 0.8761 (mt) REVERT: b 48 LYS cc_start: 0.8965 (ptpp) cc_final: 0.8228 (pttm) REVERT: b 51 LEU cc_start: 0.8906 (mt) cc_final: 0.8517 (mt) REVERT: b 54 ASN cc_start: 0.7933 (m110) cc_final: 0.7559 (m110) REVERT: b 66 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8100 (mp) REVERT: b 70 ILE cc_start: 0.8811 (mt) cc_final: 0.8604 (mt) REVERT: b 72 LYS cc_start: 0.8748 (mmtt) cc_final: 0.8251 (mtpt) REVERT: b 80 PHE cc_start: 0.8513 (t80) cc_final: 0.7868 (t80) REVERT: b 90 LYS cc_start: 0.8207 (mttm) cc_final: 0.7946 (mmmm) REVERT: b 107 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7448 (mt-10) REVERT: b 112 LEU cc_start: 0.8129 (mp) cc_final: 0.7394 (mp) REVERT: b 121 GLN cc_start: 0.8081 (tt0) cc_final: 0.7742 (mt0) REVERT: b 132 ARG cc_start: 0.8397 (mtt180) cc_final: 0.8111 (mtm180) REVERT: b 147 ILE cc_start: 0.8413 (pt) cc_final: 0.7687 (pt) REVERT: b 150 ILE cc_start: 0.8214 (mt) cc_final: 0.7815 (mt) REVERT: b 151 MET cc_start: 0.7625 (mtp) cc_final: 0.6894 (mtp) REVERT: b 162 LEU cc_start: 0.7809 (mt) cc_final: 0.7069 (tp) REVERT: b 190 GLU cc_start: 0.8133 (tt0) cc_final: 0.7867 (tt0) REVERT: b 195 LEU cc_start: 0.9048 (mt) cc_final: 0.8698 (mt) REVERT: b 202 LEU cc_start: 0.7605 (mm) cc_final: 0.7185 (tp) REVERT: b 207 VAL cc_start: 0.8831 (t) cc_final: 0.8440 (p) REVERT: b 228 LYS cc_start: 0.8584 (ttpt) cc_final: 0.8140 (ttpt) REVERT: b 244 ILE cc_start: 0.9053 (mt) cc_final: 0.8645 (tp) REVERT: b 247 MET cc_start: 0.7213 (tmm) cc_final: 0.6772 (tmm) REVERT: b 298 ARG cc_start: 0.8870 (mmm160) cc_final: 0.8029 (mpt180) REVERT: b 301 ILE cc_start: 0.8766 (mt) cc_final: 0.8495 (mt) REVERT: b 302 ARG cc_start: 0.8775 (ttm-80) cc_final: 0.8233 (mpt180) REVERT: b 307 LEU cc_start: 0.8877 (mt) cc_final: 0.8433 (mt) REVERT: b 308 LEU cc_start: 0.8765 (mt) cc_final: 0.8425 (mm) REVERT: b 311 ARG cc_start: 0.8318 (ptt180) cc_final: 0.7777 (ptt-90) REVERT: b 317 MET cc_start: 0.8663 (tpp) cc_final: 0.8303 (tpp) REVERT: b 321 GLN cc_start: 0.7946 (tt0) cc_final: 0.7449 (tt0) REVERT: b 324 TRP cc_start: 0.8646 (t-100) cc_final: 0.8012 (t-100) REVERT: b 341 ARG cc_start: 0.8644 (ptt90) cc_final: 0.7945 (ttp80) REVERT: b 352 ILE cc_start: 0.8651 (mm) cc_final: 0.8449 (mm) REVERT: b 367 MET cc_start: 0.7035 (mmp) cc_final: 0.6631 (mmt) REVERT: b 384 MET cc_start: 0.7945 (ptt) cc_final: 0.7440 (ptt) REVERT: b 386 LYS cc_start: 0.8542 (mtpt) cc_final: 0.8300 (mtpt) REVERT: b 417 ASP cc_start: 0.7808 (t0) cc_final: 0.7306 (t0) REVERT: m 1 MET cc_start: 0.7218 (mtt) cc_final: 0.6837 (mtt) REVERT: m 17 GLU cc_start: 0.7493 (pt0) cc_final: 0.7221 (pt0) REVERT: m 21 LYS cc_start: 0.7927 (mttt) cc_final: 0.7433 (mttm) REVERT: m 29 CYS cc_start: 0.8498 (m) cc_final: 0.7933 (t) REVERT: m 36 GLN cc_start: 0.8340 (tp-100) cc_final: 0.7965 (tp-100) REVERT: m 37 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8447 (tm-30) REVERT: m 43 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7495 (mt-10) REVERT: m 44 ASN cc_start: 0.8285 (t0) cc_final: 0.7515 (t0) REVERT: m 45 VAL cc_start: 0.8868 (t) cc_final: 0.8628 (t) REVERT: m 71 GLN cc_start: 0.8333 (tp40) cc_final: 0.7880 (tp40) REVERT: m 74 VAL cc_start: 0.9059 (t) cc_final: 0.8802 (t) REVERT: m 80 ILE cc_start: 0.8511 (mt) cc_final: 0.8230 (mm) REVERT: m 89 THR cc_start: 0.8876 (m) cc_final: 0.8597 (p) REVERT: m 108 ILE cc_start: 0.8909 (mt) cc_final: 0.8526 (mm) REVERT: m 111 GLU cc_start: 0.8048 (tt0) cc_final: 0.7748 (tt0) REVERT: m 116 MET cc_start: 0.7718 (mtm) cc_final: 0.7372 (mtm) REVERT: m 128 ASN cc_start: 0.8281 (m-40) cc_final: 0.8017 (m-40) REVERT: m 129 ILE cc_start: 0.8908 (mm) cc_final: 0.8605 (tp) REVERT: m 131 LYS cc_start: 0.8724 (mttp) cc_final: 0.8439 (mttt) REVERT: m 134 ILE cc_start: 0.8082 (mt) cc_final: 0.7416 (tp) REVERT: m 140 LEU cc_start: 0.8496 (mt) cc_final: 0.8228 (tt) REVERT: m 141 ARG cc_start: 0.8135 (mmt90) cc_final: 0.7733 (mmt90) REVERT: m 161 GLN cc_start: 0.8340 (tp40) cc_final: 0.8098 (tp-100) REVERT: m 209 CYS cc_start: 0.7330 (t) cc_final: 0.6458 (m) REVERT: m 220 LEU cc_start: 0.8160 (mm) cc_final: 0.7798 (mm) REVERT: m 234 HIS cc_start: 0.8045 (t-90) cc_final: 0.7735 (t-90) REVERT: m 239 PHE cc_start: 0.7796 (p90) cc_final: 0.7539 (p90) REVERT: m 240 LYS cc_start: 0.8593 (mttt) cc_final: 0.7755 (mmmm) REVERT: m 243 GLU cc_start: 0.8573 (tp30) cc_final: 0.8168 (tp30) REVERT: m 257 PHE cc_start: 0.8507 (p90) cc_final: 0.8196 (p90) REVERT: m 258 ARG cc_start: 0.8395 (mtm180) cc_final: 0.7979 (mtm180) REVERT: m 262 TYR cc_start: 0.8176 (p90) cc_final: 0.6990 (p90) REVERT: m 298 LYS cc_start: 0.9071 (tttt) cc_final: 0.8702 (tttt) REVERT: m 300 ASN cc_start: 0.9060 (p0) cc_final: 0.8747 (p0) REVERT: m 387 LEU cc_start: 0.8679 (tp) cc_final: 0.7718 (pt) REVERT: m 393 ASP cc_start: 0.8076 (t0) cc_final: 0.7694 (t0) REVERT: m 402 PHE cc_start: 0.7665 (m-80) cc_final: 0.7175 (m-80) REVERT: m 406 LYS cc_start: 0.8616 (ttmt) cc_final: 0.8350 (ttmt) REVERT: m 407 TYR cc_start: 0.8654 (m-80) cc_final: 0.7985 (m-80) REVERT: m 414 PHE cc_start: 0.7895 (t80) cc_final: 0.7428 (t80) REVERT: c 18 MET cc_start: 0.6327 (mmt) cc_final: 0.6085 (mmt) REVERT: c 30 LYS cc_start: 0.8084 (mtmm) cc_final: 0.7302 (mtmm) REVERT: c 58 TYR cc_start: 0.8226 (t80) cc_final: 0.7263 (t80) REVERT: c 64 THR cc_start: 0.6613 (m) cc_final: 0.6269 (t) REVERT: c 68 VAL cc_start: 0.8268 (t) cc_final: 0.7923 (p) REVERT: c 78 TRP cc_start: 0.8255 (m-10) cc_final: 0.7958 (m-10) REVERT: c 81 TYR cc_start: 0.7121 (m-80) cc_final: 0.6751 (m-80) REVERT: c 82 PHE cc_start: 0.8106 (m-10) cc_final: 0.7851 (m-80) REVERT: c 84 ASN cc_start: 0.8328 (t0) cc_final: 0.7568 (t0) REVERT: c 110 MET cc_start: 0.8465 (mmm) cc_final: 0.7890 (mmm) REVERT: c 115 GLU cc_start: 0.7775 (tt0) cc_final: 0.7541 (tt0) REVERT: c 145 LEU cc_start: 0.8298 (mt) cc_final: 0.7984 (mt) REVERT: c 151 ARG cc_start: 0.8406 (ttm-80) cc_final: 0.7946 (ttm-80) REVERT: c 152 ASN cc_start: 0.7821 (t0) cc_final: 0.7375 (t0) REVERT: c 167 TYR cc_start: 0.8038 (m-10) cc_final: 0.7233 (m-80) REVERT: c 168 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7698 (mt-10) REVERT: c 171 ASP cc_start: 0.8167 (m-30) cc_final: 0.7824 (m-30) REVERT: c 176 GLN cc_start: 0.8869 (mt0) cc_final: 0.8299 (mt0) REVERT: y 415 GLN cc_start: 0.7852 (mm110) cc_final: 0.7543 (mm110) outliers start: 1 outliers final: 0 residues processed: 751 average time/residue: 0.3100 time to fit residues: 328.4846 Evaluate side-chains 730 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 729 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 158 optimal weight: 0.0970 chunk 143 optimal weight: 0.5980 chunk 110 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 159 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 171 optimal weight: 30.0000 chunk 114 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 321 GLN B 355 GLN ** B 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 321 GLN ** b 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3812 r_free = 0.3812 target = 0.140406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.115700 restraints weight = 30586.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.120076 restraints weight = 16657.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.123095 restraints weight = 10423.241| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16108 Z= 0.135 Angle : 0.560 6.273 21822 Z= 0.296 Chirality : 0.044 0.174 2524 Planarity : 0.004 0.041 2752 Dihedral : 9.900 166.449 2154 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.20), residues: 1954 helix: 1.17 (0.18), residues: 810 sheet: 0.24 (0.27), residues: 382 loop : 1.02 (0.25), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP C 172 HIS 0.003 0.001 HIS M 313 PHE 0.028 0.002 PHE C 51 TYR 0.030 0.002 TYR M 110 ARG 0.008 0.000 ARG C 149 Details of bonding type rmsd hydrogen bonds : bond 0.04096 ( 815) hydrogen bonds : angle 5.03535 ( 2361) covalent geometry : bond 0.00272 (16108) covalent geometry : angle 0.56005 (21822) *********************** 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 768 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 768 time to evaluate : 1.645 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: 0.8210 (mttt) cc_final: 0.7606 (mmmt) REVERT: B 47 LEU cc_start: 0.8947 (mt) cc_final: 0.8611 (mt) REVERT: B 50 MET cc_start: 0.8598 (mtm) cc_final: 0.8136 (mtm) REVERT: B 51 LEU cc_start: 0.8807 (mt) cc_final: 0.8414 (mt) REVERT: B 52 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7592 (mm-30) REVERT: B 63 MET cc_start: 0.8516 (mmm) cc_final: 0.8010 (mmm) REVERT: B 66 ILE cc_start: 0.8517 (mm) cc_final: 0.8297 (mm) REVERT: B 70 ILE cc_start: 0.8677 (mt) cc_final: 0.8475 (mt) REVERT: B 72 LYS cc_start: 0.8888 (mmtt) cc_final: 0.8658 (ttmt) REVERT: B 74 LYS cc_start: 0.8768 (mmtt) cc_final: 0.8379 (mmtt) REVERT: B 80 PHE cc_start: 0.8604 (t80) cc_final: 0.8031 (t80) REVERT: B 85 LYS cc_start: 0.8565 (mttt) cc_final: 0.7819 (mttt) REVERT: B 90 LYS cc_start: 0.8489 (mttt) cc_final: 0.7710 (mmmm) REVERT: B 97 LEU cc_start: 0.8639 (mt) cc_final: 0.8277 (mt) REVERT: B 112 LEU cc_start: 0.8301 (mp) cc_final: 0.7488 (mp) REVERT: B 121 GLN cc_start: 0.8340 (tt0) cc_final: 0.8037 (tt0) REVERT: B 125 LYS cc_start: 0.8860 (mttt) cc_final: 0.8401 (mtpp) REVERT: B 132 ARG cc_start: 0.8258 (mtt180) cc_final: 0.8036 (mtm180) REVERT: B 137 ARG cc_start: 0.7783 (mtp-110) cc_final: 0.7558 (mtp-110) REVERT: B 147 ILE cc_start: 0.8376 (pt) cc_final: 0.7482 (pt) REVERT: B 151 MET cc_start: 0.7786 (mtp) cc_final: 0.7161 (mtp) REVERT: B 155 ILE cc_start: 0.9225 (mm) cc_final: 0.8884 (mm) REVERT: B 169 ASN cc_start: 0.8633 (m-40) cc_final: 0.8378 (m-40) REVERT: B 175 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8016 (tm-30) REVERT: B 181 ASP cc_start: 0.8440 (t0) cc_final: 0.7916 (t0) REVERT: B 186 GLU cc_start: 0.8242 (pm20) cc_final: 0.8003 (pm20) REVERT: B 190 GLU cc_start: 0.8106 (tt0) cc_final: 0.7804 (tt0) REVERT: B 193 GLU cc_start: 0.8432 (tt0) cc_final: 0.8050 (tt0) REVERT: B 196 LEU cc_start: 0.8967 (tp) cc_final: 0.8763 (tp) REVERT: B 199 LYS cc_start: 0.7982 (mppt) cc_final: 0.7698 (mmtm) REVERT: B 202 LEU cc_start: 0.7421 (mm) cc_final: 0.7001 (tp) REVERT: B 207 VAL cc_start: 0.8751 (t) cc_final: 0.8496 (p) REVERT: B 213 GLU cc_start: 0.8138 (tt0) cc_final: 0.7614 (tt0) REVERT: B 215 CYS cc_start: 0.8899 (m) cc_final: 0.8238 (p) REVERT: B 228 LYS cc_start: 0.8642 (ttpt) cc_final: 0.8123 (ttpt) REVERT: B 247 MET cc_start: 0.7299 (tmm) cc_final: 0.6745 (tmm) REVERT: B 302 ARG cc_start: 0.8485 (ttm110) cc_final: 0.8269 (ttm-80) REVERT: B 305 LYS cc_start: 0.8727 (tttt) cc_final: 0.8450 (tttm) REVERT: B 308 LEU cc_start: 0.8582 (mt) cc_final: 0.8246 (mm) REVERT: B 311 ARG cc_start: 0.8183 (ptt180) cc_final: 0.7575 (ptt-90) REVERT: B 317 MET cc_start: 0.8589 (tpp) cc_final: 0.8174 (tpp) REVERT: B 321 GLN cc_start: 0.8130 (tt0) cc_final: 0.7551 (tt0) REVERT: B 324 TRP cc_start: 0.8764 (t-100) cc_final: 0.8306 (t-100) REVERT: B 341 ARG cc_start: 0.8693 (ptt90) cc_final: 0.8262 (ptm-80) REVERT: B 360 MET cc_start: 0.8525 (tpp) cc_final: 0.7059 (tpp) REVERT: B 367 MET cc_start: 0.6969 (mtp) cc_final: 0.6738 (mtp) REVERT: B 387 THR cc_start: 0.8250 (m) cc_final: 0.7849 (m) REVERT: B 388 LEU cc_start: 0.8762 (mt) cc_final: 0.8279 (mm) REVERT: B 391 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7102 (mt-10) REVERT: B 417 ASP cc_start: 0.8403 (m-30) cc_final: 0.8175 (m-30) REVERT: M 1 MET cc_start: 0.6926 (mpp) cc_final: 0.6219 (mpp) REVERT: M 17 GLU cc_start: 0.7451 (pt0) cc_final: 0.7060 (pt0) REVERT: M 21 LYS cc_start: 0.7914 (mttt) cc_final: 0.7164 (mttm) REVERT: M 29 CYS cc_start: 0.8609 (t) cc_final: 0.8182 (t) REVERT: M 34 GLU cc_start: 0.8988 (tt0) cc_final: 0.8606 (tt0) REVERT: M 43 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7448 (mt-10) REVERT: M 78 PHE cc_start: 0.8736 (t80) cc_final: 0.8501 (t80) REVERT: M 88 ASP cc_start: 0.8520 (m-30) cc_final: 0.8237 (m-30) REVERT: M 89 THR cc_start: 0.9010 (m) cc_final: 0.8717 (p) REVERT: M 92 ASP cc_start: 0.8251 (t0) cc_final: 0.7997 (t0) REVERT: M 116 MET cc_start: 0.7870 (mtm) cc_final: 0.7492 (mtm) REVERT: M 119 ASN cc_start: 0.8195 (t0) cc_final: 0.7671 (t0) REVERT: M 123 LEU cc_start: 0.8581 (tp) cc_final: 0.8368 (tp) REVERT: M 125 THR cc_start: 0.8756 (m) cc_final: 0.8329 (t) REVERT: M 126 GLU cc_start: 0.8193 (tp30) cc_final: 0.7627 (tp30) REVERT: M 128 ASN cc_start: 0.8326 (m-40) cc_final: 0.8043 (m110) REVERT: M 131 LYS cc_start: 0.8522 (mtmm) cc_final: 0.8031 (mttp) REVERT: M 135 LYS cc_start: 0.8916 (mmtt) cc_final: 0.8463 (mmtt) REVERT: M 157 LEU cc_start: 0.8438 (mt) cc_final: 0.8162 (pp) REVERT: M 159 THR cc_start: 0.8128 (m) cc_final: 0.7912 (p) REVERT: M 161 GLN cc_start: 0.8390 (tp40) cc_final: 0.8101 (tp-100) REVERT: M 203 GLN cc_start: 0.7249 (mm-40) cc_final: 0.6883 (mm-40) REVERT: M 209 CYS cc_start: 0.7293 (t) cc_final: 0.6405 (m) REVERT: M 220 LEU cc_start: 0.8253 (mm) cc_final: 0.7851 (mm) REVERT: M 234 HIS cc_start: 0.7986 (t-90) cc_final: 0.7728 (t-90) REVERT: M 242 TRP cc_start: 0.7701 (t-100) cc_final: 0.7220 (t-100) REVERT: M 245 GLU cc_start: 0.6762 (mm-30) cc_final: 0.6168 (mm-30) REVERT: M 257 PHE cc_start: 0.8432 (p90) cc_final: 0.8153 (p90) REVERT: M 258 ARG cc_start: 0.8237 (mtm180) cc_final: 0.7829 (mtm180) REVERT: M 298 LYS cc_start: 0.9022 (tttt) cc_final: 0.8632 (tttt) REVERT: M 377 PHE cc_start: 0.7844 (p90) cc_final: 0.7539 (p90) REVERT: M 393 ASP cc_start: 0.7919 (t0) cc_final: 0.7491 (t0) REVERT: M 402 PHE cc_start: 0.7706 (m-80) cc_final: 0.7171 (m-80) REVERT: M 414 PHE cc_start: 0.7813 (t80) cc_final: 0.7257 (t80) REVERT: C 23 VAL cc_start: 0.8782 (m) cc_final: 0.8323 (m) REVERT: C 44 THR cc_start: 0.9130 (m) cc_final: 0.8733 (p) REVERT: C 64 THR cc_start: 0.6643 (m) cc_final: 0.6428 (t) REVERT: C 68 VAL cc_start: 0.8168 (t) cc_final: 0.7875 (p) REVERT: C 78 TRP cc_start: 0.8268 (m-10) cc_final: 0.7871 (m-10) REVERT: C 81 TYR cc_start: 0.7172 (m-80) cc_final: 0.6613 (m-80) REVERT: C 84 ASN cc_start: 0.8529 (t0) cc_final: 0.7751 (t0) REVERT: C 95 ASN cc_start: 0.7723 (t0) cc_final: 0.7406 (t0) REVERT: C 110 MET cc_start: 0.8615 (mmm) cc_final: 0.8069 (mmm) REVERT: C 115 GLU cc_start: 0.8072 (tt0) cc_final: 0.7759 (tt0) REVERT: C 116 LEU cc_start: 0.8025 (mt) cc_final: 0.7627 (mt) REVERT: C 142 LYS cc_start: 0.8977 (mttm) cc_final: 0.8723 (mttm) REVERT: C 145 LEU cc_start: 0.8089 (mt) cc_final: 0.7877 (mt) REVERT: C 168 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7520 (mt-10) REVERT: C 171 ASP cc_start: 0.7887 (m-30) cc_final: 0.7674 (m-30) REVERT: C 178 ARG cc_start: 0.7801 (ttm170) cc_final: 0.7584 (ttm170) REVERT: b 43 LYS cc_start: 0.8221 (mttt) cc_final: 0.7722 (tttp) REVERT: b 47 LEU cc_start: 0.9005 (mt) cc_final: 0.8553 (mt) REVERT: b 50 MET cc_start: 0.8491 (mtm) cc_final: 0.8110 (mtm) REVERT: b 51 LEU cc_start: 0.8788 (mt) cc_final: 0.8426 (mt) REVERT: b 52 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7889 (mm-30) REVERT: b 54 ASN cc_start: 0.7980 (m110) cc_final: 0.7641 (m110) REVERT: b 55 LYS cc_start: 0.8365 (mtpt) cc_final: 0.8124 (mtpt) REVERT: b 66 ILE cc_start: 0.8367 (mp) cc_final: 0.8053 (mp) REVERT: b 72 LYS cc_start: 0.8771 (mmtt) cc_final: 0.8239 (mtmt) REVERT: b 80 PHE cc_start: 0.8506 (t80) cc_final: 0.7902 (t80) REVERT: b 90 LYS cc_start: 0.8333 (mttm) cc_final: 0.8061 (mmmm) REVERT: b 101 TYR cc_start: 0.8818 (t80) cc_final: 0.8616 (t80) REVERT: b 107 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7482 (mt-10) REVERT: b 112 LEU cc_start: 0.8062 (mp) cc_final: 0.7312 (mp) REVERT: b 132 ARG cc_start: 0.8383 (mtt180) cc_final: 0.8061 (mtm180) REVERT: b 142 ILE cc_start: 0.9178 (mm) cc_final: 0.8895 (mp) REVERT: b 147 ILE cc_start: 0.8423 (pt) cc_final: 0.7700 (pt) REVERT: b 150 ILE cc_start: 0.8248 (mt) cc_final: 0.8032 (mt) REVERT: b 151 MET cc_start: 0.7600 (mtp) cc_final: 0.6913 (mtp) REVERT: b 152 MET cc_start: 0.8033 (tpt) cc_final: 0.7821 (tpt) REVERT: b 162 LEU cc_start: 0.7956 (mt) cc_final: 0.7139 (tp) REVERT: b 190 GLU cc_start: 0.8059 (tt0) cc_final: 0.7776 (tt0) REVERT: b 193 GLU cc_start: 0.8453 (tt0) cc_final: 0.8050 (tt0) REVERT: b 195 LEU cc_start: 0.8982 (mt) cc_final: 0.8639 (mt) REVERT: b 199 LYS cc_start: 0.8232 (mppt) cc_final: 0.8025 (mmtm) REVERT: b 202 LEU cc_start: 0.7649 (mm) cc_final: 0.7194 (tp) REVERT: b 207 VAL cc_start: 0.8732 (t) cc_final: 0.8410 (p) REVERT: b 228 LYS cc_start: 0.8626 (ttpt) cc_final: 0.8209 (ttpt) REVERT: b 244 ILE cc_start: 0.9118 (mt) cc_final: 0.8669 (tp) REVERT: b 247 MET cc_start: 0.7461 (tmm) cc_final: 0.6837 (tmm) REVERT: b 298 ARG cc_start: 0.8877 (mmm160) cc_final: 0.8008 (mpt180) REVERT: b 302 ARG cc_start: 0.8797 (ttm-80) cc_final: 0.8201 (mpt180) REVERT: b 307 LEU cc_start: 0.8892 (mt) cc_final: 0.8551 (mt) REVERT: b 308 LEU cc_start: 0.8747 (mt) cc_final: 0.8386 (mm) REVERT: b 311 ARG cc_start: 0.8302 (ptt180) cc_final: 0.7705 (ptt-90) REVERT: b 317 MET cc_start: 0.8660 (tpp) cc_final: 0.8321 (tpp) REVERT: b 321 GLN cc_start: 0.8023 (tt0) cc_final: 0.7506 (tt0) REVERT: b 324 TRP cc_start: 0.8674 (t-100) cc_final: 0.8202 (t-100) REVERT: b 326 ILE cc_start: 0.7950 (mm) cc_final: 0.7705 (mm) REVERT: b 331 GLU cc_start: 0.7149 (mp0) cc_final: 0.6866 (mp0) REVERT: b 341 ARG cc_start: 0.8601 (ptt90) cc_final: 0.7960 (ptm-80) REVERT: b 346 ASN cc_start: 0.7199 (p0) cc_final: 0.6619 (p0) REVERT: b 352 ILE cc_start: 0.8677 (mm) cc_final: 0.8472 (mm) REVERT: b 367 MET cc_start: 0.7097 (mmp) cc_final: 0.6739 (mmt) REVERT: b 386 LYS cc_start: 0.8556 (mtpt) cc_final: 0.8276 (mtpt) REVERT: b 417 ASP cc_start: 0.7854 (t0) cc_final: 0.7386 (t0) REVERT: m 29 CYS cc_start: 0.8496 (m) cc_final: 0.7927 (t) REVERT: m 36 GLN cc_start: 0.8337 (tp-100) cc_final: 0.7945 (tp-100) REVERT: m 37 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8485 (tm-30) REVERT: m 44 ASN cc_start: 0.8305 (t0) cc_final: 0.7865 (t0) REVERT: m 45 VAL cc_start: 0.8870 (t) cc_final: 0.8666 (t) REVERT: m 71 GLN cc_start: 0.8326 (tp40) cc_final: 0.7956 (tp40) REVERT: m 80 ILE cc_start: 0.8562 (mt) cc_final: 0.8278 (mm) REVERT: m 81 GLU cc_start: 0.7971 (tp30) cc_final: 0.7767 (tp30) REVERT: m 88 ASP cc_start: 0.8437 (m-30) cc_final: 0.8199 (m-30) REVERT: m 108 ILE cc_start: 0.8911 (mt) cc_final: 0.8603 (mm) REVERT: m 111 GLU cc_start: 0.8035 (tt0) cc_final: 0.7793 (tt0) REVERT: m 116 MET cc_start: 0.7710 (mtm) cc_final: 0.7455 (mtm) REVERT: m 123 LEU cc_start: 0.8461 (tp) cc_final: 0.8234 (tp) REVERT: m 126 GLU cc_start: 0.8313 (tp30) cc_final: 0.7540 (tp30) REVERT: m 128 ASN cc_start: 0.8307 (m-40) cc_final: 0.7660 (m-40) REVERT: m 129 ILE cc_start: 0.8869 (mm) cc_final: 0.8548 (tp) REVERT: m 134 ILE cc_start: 0.8289 (mt) cc_final: 0.8050 (tp) REVERT: m 141 ARG cc_start: 0.8170 (mmt90) cc_final: 0.7812 (mmt90) REVERT: m 161 GLN cc_start: 0.8337 (tp40) cc_final: 0.8065 (tp-100) REVERT: m 209 CYS cc_start: 0.7445 (t) cc_final: 0.6564 (m) REVERT: m 220 LEU cc_start: 0.8194 (mm) cc_final: 0.7915 (mm) REVERT: m 234 HIS cc_start: 0.8136 (t-90) cc_final: 0.7723 (t-90) REVERT: m 239 PHE cc_start: 0.7805 (p90) cc_final: 0.7580 (p90) REVERT: m 240 LYS cc_start: 0.8616 (mttt) cc_final: 0.7764 (mmmm) REVERT: m 243 GLU cc_start: 0.8615 (tp30) cc_final: 0.8272 (tp30) REVERT: m 250 PHE cc_start: 0.6826 (p90) cc_final: 0.6625 (p90) REVERT: m 257 PHE cc_start: 0.8514 (p90) cc_final: 0.8192 (p90) REVERT: m 258 ARG cc_start: 0.8418 (mtm180) cc_final: 0.8032 (mtm180) REVERT: m 262 TYR cc_start: 0.8182 (p90) cc_final: 0.7099 (p90) REVERT: m 298 LYS cc_start: 0.9061 (tttt) cc_final: 0.8705 (tttt) REVERT: m 377 PHE cc_start: 0.7760 (p90) cc_final: 0.7515 (p90) REVERT: m 378 LYS cc_start: 0.8156 (pttt) cc_final: 0.7742 (ptmm) REVERT: m 387 LEU cc_start: 0.8695 (tp) cc_final: 0.8430 (tp) REVERT: m 393 ASP cc_start: 0.8041 (t0) cc_final: 0.7668 (t0) REVERT: m 406 LYS cc_start: 0.8614 (ttmt) cc_final: 0.8355 (ttmt) REVERT: m 407 TYR cc_start: 0.8622 (m-80) cc_final: 0.8031 (m-80) REVERT: m 414 PHE cc_start: 0.7878 (t80) cc_final: 0.7515 (t80) REVERT: c 30 LYS cc_start: 0.8011 (mtmm) cc_final: 0.7311 (mtmm) REVERT: c 53 VAL cc_start: 0.8613 (t) cc_final: 0.8353 (m) REVERT: c 58 TYR cc_start: 0.8277 (t80) cc_final: 0.7383 (t80) REVERT: c 64 THR cc_start: 0.6616 (m) cc_final: 0.6214 (t) REVERT: c 68 VAL cc_start: 0.8255 (t) cc_final: 0.7957 (p) REVERT: c 82 PHE cc_start: 0.8046 (m-10) cc_final: 0.7799 (m-80) REVERT: c 84 ASN cc_start: 0.8415 (t0) cc_final: 0.7594 (t0) REVERT: c 86 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7116 (mt0) REVERT: c 110 MET cc_start: 0.8502 (mmm) cc_final: 0.7961 (mmm) REVERT: c 115 GLU cc_start: 0.7785 (tt0) cc_final: 0.7499 (tt0) REVERT: c 153 TRP cc_start: 0.8395 (p-90) cc_final: 0.8177 (p-90) REVERT: c 167 TYR cc_start: 0.8056 (m-10) cc_final: 0.7184 (m-10) REVERT: c 171 ASP cc_start: 0.8091 (m-30) cc_final: 0.7663 (m-30) REVERT: c 172 TRP cc_start: 0.8158 (t60) cc_final: 0.7436 (t60) REVERT: y 415 GLN cc_start: 0.7751 (mm110) cc_final: 0.7400 (mm110) outliers start: 0 outliers final: 0 residues processed: 768 average time/residue: 0.3122 time to fit residues: 339.6936 Evaluate side-chains 734 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 734 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 55 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 153 optimal weight: 0.3980 chunk 167 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 68 optimal weight: 0.1980 chunk 147 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 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 321 GLN B 355 GLN ** M 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 203 GLN m 26 GLN m 376 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 = 0.3772 r_free = 0.3772 target = 0.136309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.112083 restraints weight = 30738.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.116404 restraints weight = 16590.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.119303 restraints weight = 10315.169| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.5062 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= 0.153 Angle : 0.577 10.682 21822 Z= 0.304 Chirality : 0.045 0.157 2524 Planarity : 0.004 0.042 2752 Dihedral : 9.706 164.565 2154 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.20), residues: 1954 helix: 1.22 (0.18), residues: 806 sheet: 0.24 (0.27), residues: 386 loop : 0.93 (0.25), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.003 TRP C 172 HIS 0.004 0.001 HIS m 84 PHE 0.025 0.002 PHE C 51 TYR 0.027 0.002 TYR B 105 ARG 0.008 0.000 ARG C 149 Details of bonding type rmsd hydrogen bonds : bond 0.04158 ( 815) hydrogen bonds : angle 5.07393 ( 2361) covalent geometry : bond 0.00302 (16108) covalent geometry : angle 0.57700 (21822) *********************** 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 760 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 760 time to evaluate : 1.751 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: 0.8163 (mttt) cc_final: 0.7600 (tptt) REVERT: B 47 LEU cc_start: 0.8963 (mt) cc_final: 0.8634 (mt) REVERT: B 50 MET cc_start: 0.8636 (mtm) cc_final: 0.8175 (mtm) REVERT: B 51 LEU cc_start: 0.8774 (mt) cc_final: 0.8349 (mt) REVERT: B 52 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7696 (mm-30) REVERT: B 54 ASN cc_start: 0.7957 (m110) cc_final: 0.7722 (m110) REVERT: B 59 LYS cc_start: 0.8863 (mtmm) cc_final: 0.8554 (mttp) REVERT: B 63 MET cc_start: 0.8582 (mmm) cc_final: 0.8104 (mmm) REVERT: B 66 ILE cc_start: 0.8553 (mm) cc_final: 0.8275 (mm) REVERT: B 72 LYS cc_start: 0.8881 (mmtt) cc_final: 0.8668 (ttmt) REVERT: B 74 LYS cc_start: 0.8702 (mmtt) cc_final: 0.8271 (mmtt) REVERT: B 80 PHE cc_start: 0.8596 (t80) cc_final: 0.7989 (t80) REVERT: B 90 LYS cc_start: 0.8536 (mttt) cc_final: 0.7721 (mmmm) REVERT: B 107 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7434 (mt-10) REVERT: B 112 LEU cc_start: 0.8358 (mp) cc_final: 0.7510 (mp) REVERT: B 125 LYS cc_start: 0.8869 (mttt) cc_final: 0.8394 (mtpp) REVERT: B 128 ASN cc_start: 0.8179 (t0) cc_final: 0.7959 (t0) REVERT: B 137 ARG cc_start: 0.7785 (mtp-110) cc_final: 0.7543 (mtp-110) REVERT: B 147 ILE cc_start: 0.8266 (pt) cc_final: 0.7546 (pt) REVERT: B 148 VAL cc_start: 0.8869 (t) cc_final: 0.8343 (t) REVERT: B 151 MET cc_start: 0.7880 (mtp) cc_final: 0.7054 (mtp) REVERT: B 155 ILE cc_start: 0.9240 (mm) cc_final: 0.8898 (mm) REVERT: B 156 LYS cc_start: 0.8764 (mttt) cc_final: 0.8556 (ttmt) REVERT: B 169 ASN cc_start: 0.8724 (m-40) cc_final: 0.8442 (m-40) REVERT: B 175 GLN cc_start: 0.8599 (tm-30) cc_final: 0.7945 (tm-30) REVERT: B 181 ASP cc_start: 0.8528 (t0) cc_final: 0.8005 (t0) REVERT: B 183 GLU cc_start: 0.8485 (mp0) cc_final: 0.8281 (mp0) REVERT: B 186 GLU cc_start: 0.8335 (pm20) cc_final: 0.8112 (pm20) REVERT: B 190 GLU cc_start: 0.8148 (tt0) cc_final: 0.7827 (tt0) REVERT: B 193 GLU cc_start: 0.8502 (tt0) cc_final: 0.8107 (tt0) REVERT: B 196 LEU cc_start: 0.8997 (tp) cc_final: 0.8686 (tp) REVERT: B 199 LYS cc_start: 0.8041 (mppt) cc_final: 0.7802 (mmtm) REVERT: B 202 LEU cc_start: 0.7476 (mm) cc_final: 0.7057 (tp) REVERT: B 207 VAL cc_start: 0.8732 (t) cc_final: 0.8470 (p) REVERT: B 213 GLU cc_start: 0.8215 (tt0) cc_final: 0.7663 (tt0) REVERT: B 215 CYS cc_start: 0.8868 (m) cc_final: 0.8400 (p) REVERT: B 221 LEU cc_start: 0.9137 (mt) cc_final: 0.8621 (pp) REVERT: B 228 LYS cc_start: 0.8665 (ttpt) cc_final: 0.8127 (ttpt) REVERT: B 237 GLU cc_start: 0.7872 (tt0) cc_final: 0.7490 (tt0) REVERT: B 241 GLN cc_start: 0.8258 (mt0) cc_final: 0.7683 (mt0) REVERT: B 244 ILE cc_start: 0.8964 (mt) cc_final: 0.8584 (tp) REVERT: B 246 HIS cc_start: 0.8360 (m-70) cc_final: 0.8133 (m-70) REVERT: B 247 MET cc_start: 0.7276 (tmm) cc_final: 0.6763 (tmm) REVERT: B 302 ARG cc_start: 0.8437 (ttm110) cc_final: 0.8153 (ttm-80) REVERT: B 305 LYS cc_start: 0.8669 (tttt) cc_final: 0.8410 (tttm) REVERT: B 308 LEU cc_start: 0.8560 (mt) cc_final: 0.8206 (mm) REVERT: B 311 ARG cc_start: 0.8152 (ptt180) cc_final: 0.7548 (ptt-90) REVERT: B 317 MET cc_start: 0.8595 (tpp) cc_final: 0.8212 (tpp) REVERT: B 324 TRP cc_start: 0.8786 (t-100) cc_final: 0.8507 (t-100) REVERT: B 341 ARG cc_start: 0.8697 (ptt90) cc_final: 0.8257 (ptm-80) REVERT: B 346 ASN cc_start: 0.7140 (p0) cc_final: 0.6636 (p0) REVERT: B 348 GLU cc_start: 0.8154 (mp0) cc_final: 0.7766 (mp0) REVERT: B 360 MET cc_start: 0.8610 (tpp) cc_final: 0.7940 (tpp) REVERT: B 367 MET cc_start: 0.7087 (mtp) cc_final: 0.6813 (mtp) REVERT: B 389 LYS cc_start: 0.8943 (mttt) cc_final: 0.8185 (mmmm) REVERT: B 417 ASP cc_start: 0.8408 (m-30) cc_final: 0.8117 (m-30) REVERT: M 1 MET cc_start: 0.6959 (mpp) cc_final: 0.6183 (mpp) REVERT: M 17 GLU cc_start: 0.7612 (pt0) cc_final: 0.7088 (pt0) REVERT: M 21 LYS cc_start: 0.7864 (mttt) cc_final: 0.7025 (mttm) REVERT: M 29 CYS cc_start: 0.8707 (t) cc_final: 0.8270 (t) REVERT: M 31 TYR cc_start: 0.8247 (m-80) cc_final: 0.7925 (m-10) REVERT: M 34 GLU cc_start: 0.9028 (tt0) cc_final: 0.8665 (tt0) REVERT: M 41 ASP cc_start: 0.8473 (t0) cc_final: 0.8213 (t0) REVERT: M 43 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7535 (mt-10) REVERT: M 78 PHE cc_start: 0.8754 (t80) cc_final: 0.8496 (t80) REVERT: M 88 ASP cc_start: 0.8516 (m-30) cc_final: 0.8253 (m-30) REVERT: M 89 THR cc_start: 0.9020 (m) cc_final: 0.8739 (p) REVERT: M 92 ASP cc_start: 0.8232 (t0) cc_final: 0.8008 (t0) REVERT: M 103 LYS cc_start: 0.7244 (mtmm) cc_final: 0.7010 (mtmm) REVERT: M 116 MET cc_start: 0.7895 (mtm) cc_final: 0.7551 (mtm) REVERT: M 119 ASN cc_start: 0.8227 (t0) cc_final: 0.7585 (t0) REVERT: M 123 LEU cc_start: 0.8570 (tp) cc_final: 0.8319 (tp) REVERT: M 126 GLU cc_start: 0.8190 (tp30) cc_final: 0.7596 (tp30) REVERT: M 128 ASN cc_start: 0.8294 (m-40) cc_final: 0.7940 (m110) REVERT: M 131 LYS cc_start: 0.8565 (mtmm) cc_final: 0.8146 (mttp) REVERT: M 135 LYS cc_start: 0.8872 (mmtt) cc_final: 0.8412 (mmtt) REVERT: M 157 LEU cc_start: 0.8441 (mt) cc_final: 0.8217 (pp) REVERT: M 161 GLN cc_start: 0.8394 (tp40) cc_final: 0.8161 (tp-100) REVERT: M 201 GLU cc_start: 0.5738 (tm-30) cc_final: 0.5383 (tm-30) REVERT: M 203 GLN cc_start: 0.7206 (mm110) cc_final: 0.6891 (mm-40) REVERT: M 209 CYS cc_start: 0.7383 (t) cc_final: 0.6525 (m) REVERT: M 220 LEU cc_start: 0.8206 (mm) cc_final: 0.7778 (mm) REVERT: M 234 HIS cc_start: 0.8044 (t-90) cc_final: 0.7640 (t-90) REVERT: M 242 TRP cc_start: 0.7743 (t-100) cc_final: 0.7226 (t-100) REVERT: M 245 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6216 (mm-30) REVERT: M 257 PHE cc_start: 0.8467 (p90) cc_final: 0.8219 (p90) REVERT: M 258 ARG cc_start: 0.8311 (mtm180) cc_final: 0.7904 (mtm180) REVERT: M 262 TYR cc_start: 0.8365 (p90) cc_final: 0.8005 (p90) REVERT: M 298 LYS cc_start: 0.9039 (tttt) cc_final: 0.8659 (tttt) REVERT: M 377 PHE cc_start: 0.7848 (p90) cc_final: 0.7606 (p90) REVERT: M 393 ASP cc_start: 0.7760 (t0) cc_final: 0.7454 (t0) REVERT: M 414 PHE cc_start: 0.7821 (t80) cc_final: 0.7175 (t80) REVERT: C 23 VAL cc_start: 0.8757 (m) cc_final: 0.8259 (m) REVERT: C 44 THR cc_start: 0.9095 (m) cc_final: 0.8695 (p) REVERT: C 64 THR cc_start: 0.6667 (m) cc_final: 0.6451 (t) REVERT: C 68 VAL cc_start: 0.8154 (t) cc_final: 0.7840 (p) REVERT: C 78 TRP cc_start: 0.8284 (m-10) cc_final: 0.7945 (m-10) REVERT: C 81 TYR cc_start: 0.7160 (m-80) cc_final: 0.6811 (m-80) REVERT: C 82 PHE cc_start: 0.8078 (m-10) cc_final: 0.7266 (m-80) REVERT: C 84 ASN cc_start: 0.8547 (t0) cc_final: 0.7853 (t0) REVERT: C 95 ASN cc_start: 0.7777 (t0) cc_final: 0.7471 (t0) REVERT: C 110 MET cc_start: 0.8600 (mmm) cc_final: 0.8203 (mmm) REVERT: C 115 GLU cc_start: 0.8048 (tt0) cc_final: 0.7707 (tt0) REVERT: C 142 LYS cc_start: 0.8998 (mttm) cc_final: 0.8771 (mttm) REVERT: C 168 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7625 (mt-10) REVERT: C 171 ASP cc_start: 0.8058 (m-30) cc_final: 0.7624 (m-30) REVERT: b 43 LYS cc_start: 0.8129 (mttt) cc_final: 0.7625 (tptm) REVERT: b 47 LEU cc_start: 0.8983 (mt) cc_final: 0.8521 (mt) REVERT: b 50 MET cc_start: 0.8556 (mtm) cc_final: 0.8185 (mtm) REVERT: b 51 LEU cc_start: 0.8799 (mt) cc_final: 0.8419 (mt) REVERT: b 52 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7925 (mm-30) REVERT: b 54 ASN cc_start: 0.7979 (m110) cc_final: 0.7772 (m110) REVERT: b 63 MET cc_start: 0.8698 (mmm) cc_final: 0.7961 (mmm) REVERT: b 70 ILE cc_start: 0.8781 (mt) cc_final: 0.8554 (mt) REVERT: b 80 PHE cc_start: 0.8462 (t80) cc_final: 0.7794 (t80) REVERT: b 112 LEU cc_start: 0.8128 (mp) cc_final: 0.7125 (mp) REVERT: b 119 THR cc_start: 0.8377 (t) cc_final: 0.8136 (m) REVERT: b 121 GLN cc_start: 0.8160 (tt0) cc_final: 0.7929 (mt0) REVERT: b 124 LEU cc_start: 0.8941 (tp) cc_final: 0.8691 (tt) REVERT: b 130 LEU cc_start: 0.8562 (tp) cc_final: 0.8290 (tp) REVERT: b 132 ARG cc_start: 0.8436 (mtt180) cc_final: 0.8151 (mtm180) REVERT: b 142 ILE cc_start: 0.9194 (mm) cc_final: 0.8912 (mp) REVERT: b 147 ILE cc_start: 0.8418 (pt) cc_final: 0.7696 (pt) REVERT: b 150 ILE cc_start: 0.8252 (mt) cc_final: 0.8035 (mt) REVERT: b 151 MET cc_start: 0.7638 (mtp) cc_final: 0.6961 (mtp) REVERT: b 152 MET cc_start: 0.8017 (tpt) cc_final: 0.7807 (tpt) REVERT: b 162 LEU cc_start: 0.7904 (mt) cc_final: 0.7133 (tp) REVERT: b 190 GLU cc_start: 0.8092 (tt0) cc_final: 0.7813 (tt0) REVERT: b 193 GLU cc_start: 0.8513 (tt0) cc_final: 0.8098 (tt0) REVERT: b 195 LEU cc_start: 0.9031 (mt) cc_final: 0.8780 (tt) REVERT: b 199 LYS cc_start: 0.8077 (mppt) cc_final: 0.7843 (mmtm) REVERT: b 202 LEU cc_start: 0.7731 (mm) cc_final: 0.7263 (tp) REVERT: b 221 LEU cc_start: 0.9231 (mt) cc_final: 0.9012 (mt) REVERT: b 228 LYS cc_start: 0.8644 (ttpt) cc_final: 0.8231 (ttpt) REVERT: b 244 ILE cc_start: 0.9087 (mt) cc_final: 0.8653 (tp) REVERT: b 307 LEU cc_start: 0.8881 (mt) cc_final: 0.8601 (mt) REVERT: b 308 LEU cc_start: 0.8808 (mt) cc_final: 0.8507 (mm) REVERT: b 311 ARG cc_start: 0.8267 (ptt180) cc_final: 0.7699 (ptt-90) REVERT: b 317 MET cc_start: 0.8643 (tpp) cc_final: 0.8324 (tpp) REVERT: b 322 LEU cc_start: 0.8503 (tt) cc_final: 0.8289 (tt) REVERT: b 324 TRP cc_start: 0.8674 (t-100) cc_final: 0.8070 (t-100) REVERT: b 326 ILE cc_start: 0.7972 (mm) cc_final: 0.7695 (mm) REVERT: b 331 GLU cc_start: 0.7072 (mp0) cc_final: 0.6719 (mp0) REVERT: b 341 ARG cc_start: 0.8649 (ptt90) cc_final: 0.8258 (ptm-80) REVERT: b 346 ASN cc_start: 0.7241 (p0) cc_final: 0.6673 (p0) REVERT: b 363 GLN cc_start: 0.8728 (mp10) cc_final: 0.8485 (mp10) REVERT: b 367 MET cc_start: 0.7185 (mmp) cc_final: 0.6868 (mmt) REVERT: b 386 LYS cc_start: 0.8656 (mtpt) cc_final: 0.8387 (mtpt) REVERT: b 391 GLU cc_start: 0.8246 (tp30) cc_final: 0.8028 (tp30) REVERT: b 417 ASP cc_start: 0.7902 (t0) cc_final: 0.7444 (t0) REVERT: b 629 LYS cc_start: 0.8326 (ttmt) cc_final: 0.8101 (ttmt) REVERT: b 640 PRO cc_start: 0.8560 (Cg_exo) cc_final: 0.8337 (Cg_endo) REVERT: m 21 LYS cc_start: 0.8033 (mttt) cc_final: 0.7526 (mttm) REVERT: m 29 CYS cc_start: 0.8579 (m) cc_final: 0.7945 (t) REVERT: m 36 GLN cc_start: 0.8407 (tp-100) cc_final: 0.8007 (tp-100) REVERT: m 44 ASN cc_start: 0.8416 (t0) cc_final: 0.7945 (t0) REVERT: m 71 GLN cc_start: 0.8300 (tp40) cc_final: 0.7995 (tp-100) REVERT: m 72 THR cc_start: 0.8488 (p) cc_final: 0.8247 (p) REVERT: m 80 ILE cc_start: 0.8561 (mt) cc_final: 0.8307 (mm) REVERT: m 81 GLU cc_start: 0.7918 (tp30) cc_final: 0.7715 (tp30) REVERT: m 88 ASP cc_start: 0.8475 (m-30) cc_final: 0.8198 (m-30) REVERT: m 108 ILE cc_start: 0.8956 (mt) cc_final: 0.8608 (mm) REVERT: m 111 GLU cc_start: 0.8123 (tt0) cc_final: 0.7884 (tt0) REVERT: m 116 MET cc_start: 0.7848 (mtm) cc_final: 0.7442 (mtm) REVERT: m 126 GLU cc_start: 0.8364 (tp30) cc_final: 0.7537 (tp30) REVERT: m 128 ASN cc_start: 0.8300 (m-40) cc_final: 0.7699 (m-40) REVERT: m 129 ILE cc_start: 0.8890 (mm) cc_final: 0.8601 (tp) REVERT: m 134 ILE cc_start: 0.8254 (mt) cc_final: 0.8026 (tp) REVERT: m 135 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8364 (mmtt) REVERT: m 141 ARG cc_start: 0.8182 (mmt90) cc_final: 0.7821 (mmt90) REVERT: m 157 LEU cc_start: 0.8458 (mt) cc_final: 0.8184 (mt) REVERT: m 161 GLN cc_start: 0.8309 (tp40) cc_final: 0.7991 (tp-100) REVERT: m 180 TYR cc_start: 0.6816 (m-10) cc_final: 0.6570 (m-10) REVERT: m 186 GLU cc_start: 0.7508 (tt0) cc_final: 0.7284 (tt0) REVERT: m 209 CYS cc_start: 0.7385 (t) cc_final: 0.6451 (m) REVERT: m 220 LEU cc_start: 0.8088 (mm) cc_final: 0.7796 (mm) REVERT: m 228 LEU cc_start: 0.8785 (mt) cc_final: 0.8291 (pp) REVERT: m 234 HIS cc_start: 0.8147 (t-90) cc_final: 0.7682 (t-90) REVERT: m 240 LYS cc_start: 0.8581 (mttt) cc_final: 0.8028 (mmmm) REVERT: m 242 TRP cc_start: 0.7640 (t-100) cc_final: 0.7334 (t-100) REVERT: m 243 GLU cc_start: 0.8647 (tp30) cc_final: 0.8303 (tp30) REVERT: m 257 PHE cc_start: 0.8510 (p90) cc_final: 0.8144 (p90) REVERT: m 258 ARG cc_start: 0.8427 (mtm180) cc_final: 0.7958 (mtm180) REVERT: m 262 TYR cc_start: 0.8182 (p90) cc_final: 0.7054 (p90) REVERT: m 298 LYS cc_start: 0.9080 (tttt) cc_final: 0.8717 (tttt) REVERT: m 373 LEU cc_start: 0.7173 (tp) cc_final: 0.6906 (tt) REVERT: m 387 LEU cc_start: 0.8706 (tp) cc_final: 0.8270 (tp) REVERT: m 393 ASP cc_start: 0.7867 (t0) cc_final: 0.7536 (t0) REVERT: m 400 LYS cc_start: 0.8943 (mmtm) cc_final: 0.8685 (mmtt) REVERT: m 402 PHE cc_start: 0.7801 (m-80) cc_final: 0.7420 (m-10) REVERT: m 403 LYS cc_start: 0.7693 (mptt) cc_final: 0.7343 (mmtm) REVERT: m 407 TYR cc_start: 0.8650 (m-80) cc_final: 0.8109 (m-80) REVERT: m 414 PHE cc_start: 0.7818 (t80) cc_final: 0.7465 (t80) REVERT: c 18 MET cc_start: 0.6574 (mmt) cc_final: 0.6356 (mmp) REVERT: c 30 LYS cc_start: 0.8006 (mtmm) cc_final: 0.7324 (mtmm) REVERT: c 44 THR cc_start: 0.9181 (m) cc_final: 0.8766 (p) REVERT: c 45 THR cc_start: 0.8746 (p) cc_final: 0.8515 (p) REVERT: c 53 VAL cc_start: 0.8618 (t) cc_final: 0.8346 (m) REVERT: c 58 TYR cc_start: 0.8281 (t80) cc_final: 0.7386 (t80) REVERT: c 64 THR cc_start: 0.6600 (m) cc_final: 0.6236 (t) REVERT: c 68 VAL cc_start: 0.8329 (t) cc_final: 0.8011 (p) REVERT: c 78 TRP cc_start: 0.8298 (m-10) cc_final: 0.7513 (m-10) REVERT: c 82 PHE cc_start: 0.8034 (m-10) cc_final: 0.7782 (m-80) REVERT: c 84 ASN cc_start: 0.8437 (t0) cc_final: 0.7527 (t0) REVERT: c 110 MET cc_start: 0.8473 (mmm) cc_final: 0.7939 (mmm) REVERT: c 115 GLU cc_start: 0.7884 (tt0) cc_final: 0.7568 (tt0) REVERT: c 134 MET cc_start: 0.7838 (mpp) cc_final: 0.7513 (mpp) REVERT: c 145 LEU cc_start: 0.8224 (mt) cc_final: 0.7921 (mt) REVERT: c 167 TYR cc_start: 0.8066 (m-10) cc_final: 0.7142 (m-10) REVERT: c 171 ASP cc_start: 0.8195 (m-30) cc_final: 0.7760 (m-30) REVERT: y 415 GLN cc_start: 0.7754 (mm110) cc_final: 0.7371 (mm110) outliers start: 0 outliers final: 0 residues processed: 760 average time/residue: 0.3045 time to fit residues: 328.5753 Evaluate side-chains 741 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 741 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 64 optimal weight: 0.1980 chunk 80 optimal weight: 0.9980 chunk 174 optimal weight: 0.9980 chunk 160 optimal weight: 0.5980 chunk 158 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 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 355 GLN ** M 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 231 ASN m 26 GLN m 380 GLN c 95 ASN ** c 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.136342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.112048 restraints weight = 30656.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.116393 restraints weight = 16689.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.119429 restraints weight = 10408.643| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16108 Z= 0.153 Angle : 0.588 13.339 21822 Z= 0.307 Chirality : 0.045 0.183 2524 Planarity : 0.004 0.043 2752 Dihedral : 9.546 162.910 2154 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.06 % Allowed : 0.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.20), residues: 1954 helix: 1.24 (0.18), residues: 812 sheet: 0.32 (0.27), residues: 390 loop : 0.94 (0.26), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.098 0.003 TRP C 172 HIS 0.003 0.001 HIS m 84 PHE 0.026 0.002 PHE m 121 TYR 0.027 0.002 TYR M 110 ARG 0.009 0.000 ARG C 149 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 815) hydrogen bonds : angle 5.07250 ( 2361) covalent geometry : bond 0.00305 (16108) covalent geometry : angle 0.58788 (21822) *********************** 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 762 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 761 time to evaluate : 1.750 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: B 43 LYS cc_start: 0.8168 (mttt) cc_final: 0.7586 (tptt) REVERT: B 47 LEU cc_start: 0.8991 (mt) cc_final: 0.8662 (mt) REVERT: B 50 MET cc_start: 0.8615 (mtm) cc_final: 0.8181 (mtm) REVERT: B 51 LEU cc_start: 0.8787 (mt) cc_final: 0.8422 (mt) REVERT: B 52 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7666 (mm-30) REVERT: B 54 ASN cc_start: 0.7984 (m110) cc_final: 0.7721 (m110) REVERT: B 59 LYS cc_start: 0.8846 (mtmm) cc_final: 0.8591 (mttp) REVERT: B 63 MET cc_start: 0.8556 (mmm) cc_final: 0.8094 (mmm) REVERT: B 66 ILE cc_start: 0.8581 (mm) cc_final: 0.8316 (mm) REVERT: B 74 LYS cc_start: 0.8748 (mmtt) cc_final: 0.8292 (mmtt) REVERT: B 80 PHE cc_start: 0.8559 (t80) cc_final: 0.8041 (t80) REVERT: B 90 LYS cc_start: 0.8536 (mttt) cc_final: 0.7744 (mmmm) REVERT: B 97 LEU cc_start: 0.8618 (mt) cc_final: 0.8214 (mm) REVERT: B 107 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7456 (mt-10) REVERT: B 112 LEU cc_start: 0.8428 (mp) cc_final: 0.7543 (mp) REVERT: B 121 GLN cc_start: 0.8313 (tt0) cc_final: 0.8078 (mt0) REVERT: B 125 LYS cc_start: 0.8888 (mttt) cc_final: 0.8453 (mtpp) REVERT: B 128 ASN cc_start: 0.8167 (t0) cc_final: 0.7858 (t0) REVERT: B 132 ARG cc_start: 0.8480 (mtm180) cc_final: 0.8133 (mtm-85) REVERT: B 137 ARG cc_start: 0.7746 (mtp-110) cc_final: 0.7370 (mtp-110) REVERT: B 147 ILE cc_start: 0.8320 (pt) cc_final: 0.7556 (pt) REVERT: B 148 VAL cc_start: 0.8860 (t) cc_final: 0.8344 (t) REVERT: B 150 ILE cc_start: 0.8381 (tp) cc_final: 0.8169 (tp) REVERT: B 151 MET cc_start: 0.7862 (mtp) cc_final: 0.7045 (mtp) REVERT: B 155 ILE cc_start: 0.9228 (mm) cc_final: 0.8871 (mm) REVERT: B 169 ASN cc_start: 0.8708 (m-40) cc_final: 0.8417 (m-40) REVERT: B 175 GLN cc_start: 0.8540 (tm-30) cc_final: 0.7894 (tm-30) REVERT: B 181 ASP cc_start: 0.8526 (t0) cc_final: 0.8030 (t0) REVERT: B 190 GLU cc_start: 0.8147 (tt0) cc_final: 0.7817 (tt0) REVERT: B 193 GLU cc_start: 0.8488 (tt0) cc_final: 0.8113 (tt0) REVERT: B 199 LYS cc_start: 0.8040 (mppt) cc_final: 0.7801 (mmtm) REVERT: B 202 LEU cc_start: 0.7530 (mm) cc_final: 0.7096 (tp) REVERT: B 207 VAL cc_start: 0.8683 (t) cc_final: 0.8405 (p) REVERT: B 213 GLU cc_start: 0.8117 (tt0) cc_final: 0.7632 (tt0) REVERT: B 215 CYS cc_start: 0.8955 (m) cc_final: 0.8485 (p) REVERT: B 221 LEU cc_start: 0.9180 (mt) cc_final: 0.8695 (pp) REVERT: B 228 LYS cc_start: 0.8687 (ttpt) cc_final: 0.8138 (ttpt) REVERT: B 246 HIS cc_start: 0.8380 (m-70) cc_final: 0.8153 (m-70) REVERT: B 247 MET cc_start: 0.7225 (tmm) cc_final: 0.6878 (tmm) REVERT: B 308 LEU cc_start: 0.8649 (mt) cc_final: 0.8267 (mm) REVERT: B 311 ARG cc_start: 0.8123 (ptt180) cc_final: 0.7534 (ptt-90) REVERT: B 317 MET cc_start: 0.8573 (tpp) cc_final: 0.8182 (tpp) REVERT: B 321 GLN cc_start: 0.8122 (tt0) cc_final: 0.7488 (tt0) REVERT: B 324 TRP cc_start: 0.8773 (t-100) cc_final: 0.8450 (t-100) REVERT: B 341 ARG cc_start: 0.8722 (ptt90) cc_final: 0.8255 (ptm-80) REVERT: B 360 MET cc_start: 0.8606 (tpp) cc_final: 0.7809 (tpp) REVERT: B 367 MET cc_start: 0.7123 (mtp) cc_final: 0.6818 (mtp) REVERT: B 389 LYS cc_start: 0.8966 (mttt) cc_final: 0.8254 (mmmm) REVERT: B 417 ASP cc_start: 0.8450 (m-30) cc_final: 0.8146 (m-30) REVERT: M 1 MET cc_start: 0.6927 (mpp) cc_final: 0.6307 (mpp) REVERT: M 17 GLU cc_start: 0.7446 (pt0) cc_final: 0.7097 (pt0) REVERT: M 21 LYS cc_start: 0.7807 (mttt) cc_final: 0.7016 (mttm) REVERT: M 29 CYS cc_start: 0.8713 (t) cc_final: 0.8239 (t) REVERT: M 34 GLU cc_start: 0.9016 (tt0) cc_final: 0.8643 (tt0) REVERT: M 41 ASP cc_start: 0.8486 (t0) cc_final: 0.8217 (t0) REVERT: M 43 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7486 (mt-10) REVERT: M 78 PHE cc_start: 0.8750 (t80) cc_final: 0.8498 (t80) REVERT: M 89 THR cc_start: 0.9030 (m) cc_final: 0.8778 (p) REVERT: M 103 LYS cc_start: 0.7205 (mtmm) cc_final: 0.7000 (mtmm) REVERT: M 116 MET cc_start: 0.7910 (mtm) cc_final: 0.7529 (mtm) REVERT: M 119 ASN cc_start: 0.8227 (t0) cc_final: 0.7628 (t0) REVERT: M 126 GLU cc_start: 0.8279 (tp30) cc_final: 0.7651 (tp30) REVERT: M 128 ASN cc_start: 0.8244 (m-40) cc_final: 0.7921 (m110) REVERT: M 131 LYS cc_start: 0.8576 (mtmm) cc_final: 0.8171 (mttp) REVERT: M 135 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8419 (mmtt) REVERT: M 157 LEU cc_start: 0.8441 (mt) cc_final: 0.8225 (pp) REVERT: M 161 GLN cc_start: 0.8410 (tp40) cc_final: 0.8125 (tp-100) REVERT: M 209 CYS cc_start: 0.7372 (t) cc_final: 0.6534 (m) REVERT: M 220 LEU cc_start: 0.8256 (mm) cc_final: 0.7839 (mm) REVERT: M 234 HIS cc_start: 0.8109 (t-90) cc_final: 0.7703 (t-90) REVERT: M 242 TRP cc_start: 0.7793 (t-100) cc_final: 0.7243 (t-100) REVERT: M 245 GLU cc_start: 0.6755 (mm-30) cc_final: 0.6239 (mm-30) REVERT: M 257 PHE cc_start: 0.8447 (p90) cc_final: 0.8005 (p90) REVERT: M 258 ARG cc_start: 0.8347 (mtm180) cc_final: 0.7820 (mtm180) REVERT: M 262 TYR cc_start: 0.8375 (p90) cc_final: 0.8059 (p90) REVERT: M 298 LYS cc_start: 0.9048 (tttt) cc_final: 0.8665 (tttt) REVERT: M 381 GLN cc_start: 0.8867 (mp10) cc_final: 0.8375 (mp10) REVERT: M 393 ASP cc_start: 0.7792 (t0) cc_final: 0.7313 (t0) REVERT: M 414 PHE cc_start: 0.7832 (t80) cc_final: 0.7217 (t80) REVERT: C 23 VAL cc_start: 0.8749 (m) cc_final: 0.8249 (m) REVERT: C 44 THR cc_start: 0.9115 (m) cc_final: 0.8680 (p) REVERT: C 68 VAL cc_start: 0.8125 (t) cc_final: 0.7826 (p) REVERT: C 78 TRP cc_start: 0.8277 (m-10) cc_final: 0.7926 (m-10) REVERT: C 81 TYR cc_start: 0.7119 (m-80) cc_final: 0.6757 (m-80) REVERT: C 82 PHE cc_start: 0.7994 (m-10) cc_final: 0.7115 (m-80) REVERT: C 84 ASN cc_start: 0.8557 (t0) cc_final: 0.7876 (t0) REVERT: C 110 MET cc_start: 0.8579 (mmm) cc_final: 0.8166 (mmm) REVERT: C 115 GLU cc_start: 0.8026 (tt0) cc_final: 0.7729 (tt0) REVERT: C 116 LEU cc_start: 0.8025 (mt) cc_final: 0.7802 (mt) REVERT: C 168 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7584 (mt-10) REVERT: C 171 ASP cc_start: 0.7833 (m-30) cc_final: 0.7625 (m-30) REVERT: C 178 ARG cc_start: 0.7340 (ttm110) cc_final: 0.6897 (ttm110) REVERT: b 43 LYS cc_start: 0.8171 (mttt) cc_final: 0.7694 (tptm) REVERT: b 45 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7460 (mm-30) REVERT: b 47 LEU cc_start: 0.9032 (mt) cc_final: 0.8546 (mt) REVERT: b 48 LYS cc_start: 0.8909 (ptpp) cc_final: 0.8050 (pttm) REVERT: b 50 MET cc_start: 0.8509 (mtm) cc_final: 0.8161 (mtm) REVERT: b 51 LEU cc_start: 0.8735 (mt) cc_final: 0.8380 (mt) REVERT: b 52 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7900 (mm-30) REVERT: b 54 ASN cc_start: 0.8007 (m110) cc_final: 0.7735 (m110) REVERT: b 80 PHE cc_start: 0.8439 (t80) cc_final: 0.7871 (t80) REVERT: b 107 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7451 (mt-10) REVERT: b 112 LEU cc_start: 0.8207 (mp) cc_final: 0.7409 (mp) REVERT: b 124 LEU cc_start: 0.8928 (tp) cc_final: 0.8685 (tt) REVERT: b 132 ARG cc_start: 0.8381 (mtt180) cc_final: 0.8101 (mtm180) REVERT: b 139 LEU cc_start: 0.8579 (tt) cc_final: 0.8373 (tt) REVERT: b 142 ILE cc_start: 0.9130 (mm) cc_final: 0.8907 (mp) REVERT: b 147 ILE cc_start: 0.8418 (pt) cc_final: 0.7661 (pt) REVERT: b 150 ILE cc_start: 0.8282 (mt) cc_final: 0.8063 (mt) REVERT: b 151 MET cc_start: 0.7621 (mtp) cc_final: 0.6947 (mtp) REVERT: b 152 MET cc_start: 0.8011 (tpt) cc_final: 0.7778 (tpt) REVERT: b 162 LEU cc_start: 0.7955 (mt) cc_final: 0.7176 (tp) REVERT: b 190 GLU cc_start: 0.8033 (tt0) cc_final: 0.7761 (tt0) REVERT: b 195 LEU cc_start: 0.8985 (mt) cc_final: 0.8756 (tt) REVERT: b 199 LYS cc_start: 0.8083 (mppt) cc_final: 0.7841 (mmtm) REVERT: b 202 LEU cc_start: 0.7764 (mm) cc_final: 0.7304 (tt) REVERT: b 228 LYS cc_start: 0.8677 (ttpt) cc_final: 0.8270 (ttpt) REVERT: b 237 GLU cc_start: 0.7596 (tt0) cc_final: 0.7106 (tt0) REVERT: b 241 GLN cc_start: 0.8127 (mt0) cc_final: 0.7571 (mt0) REVERT: b 244 ILE cc_start: 0.9107 (mt) cc_final: 0.8668 (tp) REVERT: b 307 LEU cc_start: 0.8883 (mt) cc_final: 0.8469 (mt) REVERT: b 308 LEU cc_start: 0.8809 (mt) cc_final: 0.8505 (mm) REVERT: b 311 ARG cc_start: 0.8285 (ptt180) cc_final: 0.7708 (ptt-90) REVERT: b 317 MET cc_start: 0.8601 (tpp) cc_final: 0.8268 (tpp) REVERT: b 321 GLN cc_start: 0.7958 (tt0) cc_final: 0.7585 (tt0) REVERT: b 322 LEU cc_start: 0.8480 (tt) cc_final: 0.8246 (tt) REVERT: b 324 TRP cc_start: 0.8674 (t-100) cc_final: 0.8296 (t-100) REVERT: b 326 ILE cc_start: 0.7938 (mm) cc_final: 0.7640 (mm) REVERT: b 331 GLU cc_start: 0.7115 (mp0) cc_final: 0.6680 (mp0) REVERT: b 341 ARG cc_start: 0.8653 (ptt90) cc_final: 0.8163 (ptm-80) REVERT: b 346 ASN cc_start: 0.7261 (p0) cc_final: 0.6631 (p0) REVERT: b 352 ILE cc_start: 0.8669 (mm) cc_final: 0.8463 (mm) REVERT: b 367 MET cc_start: 0.7328 (mmp) cc_final: 0.7108 (mmt) REVERT: b 386 LYS cc_start: 0.8599 (mtpt) cc_final: 0.8327 (mtpt) REVERT: b 391 GLU cc_start: 0.8255 (tp30) cc_final: 0.8038 (tp30) REVERT: b 417 ASP cc_start: 0.7944 (t0) cc_final: 0.7469 (t0) REVERT: b 629 LYS cc_start: 0.8361 (ttmt) cc_final: 0.8135 (ttmt) REVERT: b 640 PRO cc_start: 0.8570 (Cg_exo) cc_final: 0.8355 (Cg_endo) REVERT: m 17 GLU cc_start: 0.7596 (pt0) cc_final: 0.7353 (pt0) REVERT: m 21 LYS cc_start: 0.8041 (mttt) cc_final: 0.7527 (mttm) REVERT: m 29 CYS cc_start: 0.8537 (m) cc_final: 0.7943 (t) REVERT: m 36 GLN cc_start: 0.8391 (tp-100) cc_final: 0.7988 (tp-100) REVERT: m 44 ASN cc_start: 0.8408 (t0) cc_final: 0.7921 (t0) REVERT: m 45 VAL cc_start: 0.8867 (t) cc_final: 0.8659 (t) REVERT: m 71 GLN cc_start: 0.8312 (tp40) cc_final: 0.8018 (tp40) REVERT: m 72 THR cc_start: 0.8529 (p) cc_final: 0.8271 (p) REVERT: m 80 ILE cc_start: 0.8616 (mt) cc_final: 0.8346 (mm) REVERT: m 81 GLU cc_start: 0.7964 (tp30) cc_final: 0.7730 (tp30) REVERT: m 88 ASP cc_start: 0.8460 (m-30) cc_final: 0.8173 (m-30) REVERT: m 108 ILE cc_start: 0.8872 (mt) cc_final: 0.8488 (mm) REVERT: m 111 GLU cc_start: 0.8050 (tt0) cc_final: 0.7820 (tt0) REVERT: m 116 MET cc_start: 0.7783 (mtm) cc_final: 0.7534 (mtm) REVERT: m 126 GLU cc_start: 0.8372 (tp30) cc_final: 0.7534 (tp30) REVERT: m 128 ASN cc_start: 0.8233 (m-40) cc_final: 0.7616 (m-40) REVERT: m 129 ILE cc_start: 0.8907 (mm) cc_final: 0.8619 (tp) REVERT: m 131 LYS cc_start: 0.8648 (mttp) cc_final: 0.8261 (mttt) REVERT: m 134 ILE cc_start: 0.8294 (mt) cc_final: 0.8037 (tp) REVERT: m 141 ARG cc_start: 0.8125 (mmt90) cc_final: 0.7783 (mmt90) REVERT: m 157 LEU cc_start: 0.8465 (mt) cc_final: 0.8167 (mt) REVERT: m 161 GLN cc_start: 0.8330 (tp40) cc_final: 0.8025 (tp-100) REVERT: m 180 TYR cc_start: 0.6874 (m-10) cc_final: 0.6609 (m-10) REVERT: m 186 GLU cc_start: 0.7495 (tt0) cc_final: 0.7294 (tt0) REVERT: m 209 CYS cc_start: 0.7424 (t) cc_final: 0.6420 (m) REVERT: m 220 LEU cc_start: 0.8136 (mm) cc_final: 0.7836 (mm) REVERT: m 234 HIS cc_start: 0.8148 (t-90) cc_final: 0.7698 (t-90) REVERT: m 240 LYS cc_start: 0.8553 (mttt) cc_final: 0.7826 (mmmm) REVERT: m 243 GLU cc_start: 0.8612 (tp30) cc_final: 0.8255 (tp30) REVERT: m 257 PHE cc_start: 0.8527 (p90) cc_final: 0.8186 (p90) REVERT: m 258 ARG cc_start: 0.8448 (mtm180) cc_final: 0.8056 (mtm180) REVERT: m 262 TYR cc_start: 0.8184 (p90) cc_final: 0.7110 (p90) REVERT: m 269 LEU cc_start: 0.7677 (mm) cc_final: 0.7375 (mp) REVERT: m 272 ILE cc_start: 0.8045 (mm) cc_final: 0.7626 (tp) REVERT: m 342 ASP cc_start: 0.7846 (t0) cc_final: 0.7451 (t0) REVERT: m 387 LEU cc_start: 0.8675 (tp) cc_final: 0.8353 (tp) REVERT: m 393 ASP cc_start: 0.7890 (t0) cc_final: 0.7542 (t0) REVERT: m 400 LYS cc_start: 0.8890 (mmtm) cc_final: 0.8633 (mmtt) REVERT: m 402 PHE cc_start: 0.7809 (m-80) cc_final: 0.7436 (m-10) REVERT: m 403 LYS cc_start: 0.7753 (mptt) cc_final: 0.7386 (mmtm) REVERT: m 407 TYR cc_start: 0.8669 (m-80) cc_final: 0.8092 (m-80) REVERT: m 414 PHE cc_start: 0.7854 (t80) cc_final: 0.7458 (t80) REVERT: c 30 LYS cc_start: 0.7922 (mtmm) cc_final: 0.7257 (mtmm) REVERT: c 44 THR cc_start: 0.9199 (m) cc_final: 0.8777 (p) REVERT: c 53 VAL cc_start: 0.8662 (t) cc_final: 0.8379 (m) REVERT: c 64 THR cc_start: 0.6561 (m) cc_final: 0.6230 (t) REVERT: c 68 VAL cc_start: 0.8327 (t) cc_final: 0.7987 (p) REVERT: c 78 TRP cc_start: 0.8327 (m-10) cc_final: 0.7990 (m-10) REVERT: c 82 PHE cc_start: 0.8057 (m-10) cc_final: 0.7762 (m-80) REVERT: c 84 ASN cc_start: 0.8458 (t0) cc_final: 0.7605 (t0) REVERT: c 86 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7350 (mt0) REVERT: c 110 MET cc_start: 0.8451 (mmm) cc_final: 0.7869 (mmm) REVERT: c 115 GLU cc_start: 0.7939 (tt0) cc_final: 0.7589 (tt0) REVERT: c 118 ASP cc_start: 0.8180 (m-30) cc_final: 0.7963 (m-30) REVERT: c 134 MET cc_start: 0.7871 (mpp) cc_final: 0.7460 (mpp) REVERT: c 145 LEU cc_start: 0.8163 (mt) cc_final: 0.7888 (mt) REVERT: c 171 ASP cc_start: 0.8094 (m-30) cc_final: 0.7700 (m-30) REVERT: y 411 HIS cc_start: 0.6090 (t70) cc_final: 0.5407 (t-170) REVERT: y 415 GLN cc_start: 0.7775 (mm110) cc_final: 0.7370 (mm110) outliers start: 1 outliers final: 0 residues processed: 761 average time/residue: 0.3100 time to fit residues: 334.4227 Evaluate side-chains 732 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 732 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 184 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 106 optimal weight: 0.0040 chunk 173 optimal weight: 0.0870 chunk 138 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 chunk 20 optimal weight: 0.5980 chunk 135 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.4570 ------------------------------------------------------------------------------- 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** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 231 ASN b 246 HIS m 26 GLN ** m 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 95 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.138560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.114266 restraints weight = 30490.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.118536 restraints weight = 16614.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.121577 restraints weight = 10450.676| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.5448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16108 Z= 0.128 Angle : 0.569 9.790 21822 Z= 0.297 Chirality : 0.045 0.167 2524 Planarity : 0.004 0.045 2752 Dihedral : 9.313 160.947 2154 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.20), residues: 1954 helix: 1.35 (0.19), residues: 812 sheet: 0.41 (0.27), residues: 386 loop : 0.94 (0.26), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP b 239 HIS 0.003 0.001 HIS m 84 PHE 0.019 0.001 PHE C 51 TYR 0.022 0.002 TYR c 58 ARG 0.009 0.000 ARG C 149 Details of bonding type rmsd hydrogen bonds : bond 0.03870 ( 815) hydrogen bonds : angle 4.92525 ( 2361) covalent geometry : bond 0.00265 (16108) covalent geometry : angle 0.56895 (21822) *********************** 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 767 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 767 time to evaluate : 1.627 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: B 43 LYS cc_start: 0.8138 (mttt) cc_final: 0.7531 (tptt) REVERT: B 47 LEU cc_start: 0.8990 (mt) cc_final: 0.8610 (mt) REVERT: B 50 MET cc_start: 0.8635 (mtm) cc_final: 0.8195 (mtm) REVERT: B 51 LEU cc_start: 0.8789 (mt) cc_final: 0.8402 (mt) REVERT: B 52 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7628 (mm-30) REVERT: B 54 ASN cc_start: 0.7971 (m110) cc_final: 0.7585 (m110) REVERT: B 59 LYS cc_start: 0.8784 (mtmm) cc_final: 0.8521 (mttt) REVERT: B 63 MET cc_start: 0.8604 (mmm) cc_final: 0.8106 (mmm) REVERT: B 74 LYS cc_start: 0.8888 (mmtt) cc_final: 0.8240 (mmtt) REVERT: B 80 PHE cc_start: 0.8576 (t80) cc_final: 0.8024 (t80) REVERT: B 85 LYS cc_start: 0.8585 (mttt) cc_final: 0.7736 (mttt) REVERT: B 90 LYS cc_start: 0.8519 (mttt) cc_final: 0.7718 (mmmm) REVERT: B 107 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7425 (mt-10) REVERT: B 112 LEU cc_start: 0.8356 (mp) cc_final: 0.7562 (mp) REVERT: B 125 LYS cc_start: 0.8911 (mttt) cc_final: 0.8448 (mtpp) REVERT: B 128 ASN cc_start: 0.8049 (t0) cc_final: 0.7725 (t0) REVERT: B 132 ARG cc_start: 0.8464 (mtm180) cc_final: 0.8097 (mtm-85) REVERT: B 137 ARG cc_start: 0.7765 (mtp-110) cc_final: 0.7233 (mtp-110) REVERT: B 147 ILE cc_start: 0.8303 (pt) cc_final: 0.7535 (pt) REVERT: B 148 VAL cc_start: 0.8805 (t) cc_final: 0.8322 (t) REVERT: B 151 MET cc_start: 0.7869 (mtp) cc_final: 0.7027 (mtp) REVERT: B 155 ILE cc_start: 0.9161 (mm) cc_final: 0.8888 (mm) REVERT: B 175 GLN cc_start: 0.8550 (tm-30) cc_final: 0.7825 (tm-30) REVERT: B 183 GLU cc_start: 0.8425 (mp0) cc_final: 0.8059 (mp0) REVERT: B 185 LYS cc_start: 0.8567 (tttp) cc_final: 0.8226 (tptp) REVERT: B 190 GLU cc_start: 0.8128 (tt0) cc_final: 0.7775 (tt0) REVERT: B 193 GLU cc_start: 0.8480 (tt0) cc_final: 0.8112 (tt0) REVERT: B 195 LEU cc_start: 0.8905 (mm) cc_final: 0.8703 (tt) REVERT: B 199 LYS cc_start: 0.7992 (mppt) cc_final: 0.7753 (mmtm) REVERT: B 202 LEU cc_start: 0.7475 (mm) cc_final: 0.7043 (tt) REVERT: B 213 GLU cc_start: 0.8223 (tt0) cc_final: 0.7687 (tt0) REVERT: B 221 LEU cc_start: 0.9193 (mt) cc_final: 0.8819 (pp) REVERT: B 228 LYS cc_start: 0.8672 (ttpt) cc_final: 0.8122 (ttpt) REVERT: B 237 GLU cc_start: 0.7834 (tt0) cc_final: 0.7483 (tt0) REVERT: B 241 GLN cc_start: 0.8183 (mt0) cc_final: 0.7756 (mt0) REVERT: B 246 HIS cc_start: 0.8327 (m-70) cc_final: 0.8111 (m-70) REVERT: B 247 MET cc_start: 0.7194 (tmm) cc_final: 0.6890 (tmm) REVERT: B 302 ARG cc_start: 0.8366 (mtt-85) cc_final: 0.7809 (ttm-80) REVERT: B 303 ASN cc_start: 0.8488 (m-40) cc_final: 0.8236 (t0) REVERT: B 307 LEU cc_start: 0.8715 (mm) cc_final: 0.8292 (tp) REVERT: B 308 LEU cc_start: 0.8636 (mt) cc_final: 0.8282 (mm) REVERT: B 317 MET cc_start: 0.8546 (tpp) cc_final: 0.8174 (tpp) REVERT: B 321 GLN cc_start: 0.8013 (tt0) cc_final: 0.7389 (tt0) REVERT: B 324 TRP cc_start: 0.8762 (t-100) cc_final: 0.8409 (t-100) REVERT: B 341 ARG cc_start: 0.8718 (ptt90) cc_final: 0.8247 (ptm-80) REVERT: B 346 ASN cc_start: 0.7094 (p0) cc_final: 0.6614 (p0) REVERT: B 348 GLU cc_start: 0.8165 (mp0) cc_final: 0.7787 (mp0) REVERT: B 367 MET cc_start: 0.7114 (mtp) cc_final: 0.6859 (mtp) REVERT: B 389 LYS cc_start: 0.8962 (mttt) cc_final: 0.8375 (ttmm) REVERT: B 391 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7554 (mt-10) REVERT: B 417 ASP cc_start: 0.8446 (m-30) cc_final: 0.8150 (m-30) REVERT: M 1 MET cc_start: 0.6874 (mpp) cc_final: 0.6242 (mpp) REVERT: M 17 GLU cc_start: 0.7608 (pt0) cc_final: 0.7007 (pt0) REVERT: M 21 LYS cc_start: 0.7796 (mttt) cc_final: 0.7000 (mttm) REVERT: M 29 CYS cc_start: 0.8689 (t) cc_final: 0.8266 (t) REVERT: M 31 TYR cc_start: 0.8249 (m-80) cc_final: 0.7791 (m-10) REVERT: M 34 GLU cc_start: 0.9023 (tt0) cc_final: 0.8620 (tt0) REVERT: M 41 ASP cc_start: 0.8534 (t0) cc_final: 0.8250 (t0) REVERT: M 43 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7530 (mt-10) REVERT: M 63 LYS cc_start: 0.8268 (mttt) cc_final: 0.7480 (tmtt) REVERT: M 89 THR cc_start: 0.9032 (m) cc_final: 0.8782 (p) REVERT: M 103 LYS cc_start: 0.7153 (mtmm) cc_final: 0.6949 (mtmm) REVERT: M 116 MET cc_start: 0.7826 (mtm) cc_final: 0.7545 (mtm) REVERT: M 119 ASN cc_start: 0.8187 (t0) cc_final: 0.7608 (t0) REVERT: M 126 GLU cc_start: 0.8288 (tp30) cc_final: 0.7665 (tp30) REVERT: M 128 ASN cc_start: 0.8206 (m-40) cc_final: 0.7893 (m110) REVERT: M 131 LYS cc_start: 0.8576 (mtmm) cc_final: 0.8170 (mttp) REVERT: M 135 LYS cc_start: 0.8873 (mmtt) cc_final: 0.8430 (mmtt) REVERT: M 157 LEU cc_start: 0.8440 (mt) cc_final: 0.8232 (pp) REVERT: M 161 GLN cc_start: 0.8376 (tp40) cc_final: 0.8098 (tp-100) REVERT: M 172 VAL cc_start: 0.8734 (t) cc_final: 0.8451 (t) REVERT: M 201 GLU cc_start: 0.5675 (tm-30) cc_final: 0.4744 (tm-30) REVERT: M 203 GLN cc_start: 0.7192 (mm110) cc_final: 0.6771 (mm-40) REVERT: M 209 CYS cc_start: 0.7372 (t) cc_final: 0.6509 (m) REVERT: M 220 LEU cc_start: 0.8212 (mm) cc_final: 0.7847 (mm) REVERT: M 234 HIS cc_start: 0.8055 (t-90) cc_final: 0.7831 (t-90) REVERT: M 242 TRP cc_start: 0.7786 (t-100) cc_final: 0.7149 (t-100) REVERT: M 245 GLU cc_start: 0.6765 (mm-30) cc_final: 0.6283 (mm-30) REVERT: M 257 PHE cc_start: 0.8457 (p90) cc_final: 0.7896 (p90) REVERT: M 258 ARG cc_start: 0.8351 (mtm180) cc_final: 0.7827 (mtm180) REVERT: M 262 TYR cc_start: 0.8348 (p90) cc_final: 0.8055 (p90) REVERT: M 298 LYS cc_start: 0.9040 (tttt) cc_final: 0.8610 (tttt) REVERT: M 393 ASP cc_start: 0.7771 (t0) cc_final: 0.7287 (t0) REVERT: M 400 LYS cc_start: 0.8878 (mmtm) cc_final: 0.8653 (mmtt) REVERT: M 402 PHE cc_start: 0.7672 (m-80) cc_final: 0.7296 (m-80) REVERT: M 414 PHE cc_start: 0.7765 (t80) cc_final: 0.7170 (t80) REVERT: C 23 VAL cc_start: 0.8743 (m) cc_final: 0.8239 (m) REVERT: C 44 THR cc_start: 0.9115 (m) cc_final: 0.8678 (p) REVERT: C 57 GLU cc_start: 0.7958 (tt0) cc_final: 0.7530 (tt0) REVERT: C 68 VAL cc_start: 0.8077 (t) cc_final: 0.7819 (p) REVERT: C 78 TRP cc_start: 0.8297 (m-10) cc_final: 0.7943 (m-10) REVERT: C 81 TYR cc_start: 0.7117 (m-80) cc_final: 0.6393 (m-80) REVERT: C 82 PHE cc_start: 0.7995 (m-10) cc_final: 0.7100 (m-80) REVERT: C 84 ASN cc_start: 0.8554 (t0) cc_final: 0.7885 (t0) REVERT: C 108 MET cc_start: 0.7787 (mtm) cc_final: 0.7489 (mtt) REVERT: C 110 MET cc_start: 0.8552 (mmm) cc_final: 0.8155 (mmm) REVERT: C 115 GLU cc_start: 0.7999 (tt0) cc_final: 0.7674 (tt0) REVERT: C 116 LEU cc_start: 0.7990 (mt) cc_final: 0.7733 (mt) REVERT: C 168 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7603 (mt-10) REVERT: C 171 ASP cc_start: 0.8048 (m-30) cc_final: 0.7672 (m-30) REVERT: C 178 ARG cc_start: 0.7448 (ttm110) cc_final: 0.6885 (ttm110) REVERT: b 43 LYS cc_start: 0.8230 (mttt) cc_final: 0.7718 (tptm) REVERT: b 47 LEU cc_start: 0.9000 (mt) cc_final: 0.8630 (mt) REVERT: b 50 MET cc_start: 0.8503 (mtm) cc_final: 0.8185 (mtm) REVERT: b 52 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7939 (mm-30) REVERT: b 72 LYS cc_start: 0.8715 (mmtt) cc_final: 0.8423 (mmtt) REVERT: b 80 PHE cc_start: 0.8409 (t80) cc_final: 0.7846 (t80) REVERT: b 101 TYR cc_start: 0.8743 (t80) cc_final: 0.8467 (t80) REVERT: b 102 LEU cc_start: 0.8916 (mt) cc_final: 0.8716 (mt) REVERT: b 107 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7406 (mt-10) REVERT: b 112 LEU cc_start: 0.8218 (mp) cc_final: 0.7427 (mp) REVERT: b 119 THR cc_start: 0.8442 (t) cc_final: 0.8145 (m) REVERT: b 121 GLN cc_start: 0.8051 (tt0) cc_final: 0.7678 (mt0) REVERT: b 124 LEU cc_start: 0.8942 (tp) cc_final: 0.8699 (tt) REVERT: b 130 LEU cc_start: 0.8502 (tp) cc_final: 0.8198 (tp) REVERT: b 132 ARG cc_start: 0.8367 (mtt180) cc_final: 0.8103 (mtm180) REVERT: b 137 ARG cc_start: 0.7828 (mtp85) cc_final: 0.7289 (mtp85) REVERT: b 142 ILE cc_start: 0.9112 (mm) cc_final: 0.8894 (mp) REVERT: b 147 ILE cc_start: 0.8400 (pt) cc_final: 0.7623 (pt) REVERT: b 150 ILE cc_start: 0.8263 (mt) cc_final: 0.7762 (mt) REVERT: b 151 MET cc_start: 0.7629 (mtp) cc_final: 0.6936 (mtp) REVERT: b 152 MET cc_start: 0.8024 (tpt) cc_final: 0.7776 (tpt) REVERT: b 162 LEU cc_start: 0.8051 (mt) cc_final: 0.7261 (tp) REVERT: b 190 GLU cc_start: 0.8017 (tt0) cc_final: 0.7739 (tt0) REVERT: b 199 LYS cc_start: 0.8052 (mppt) cc_final: 0.7806 (mmtm) REVERT: b 202 LEU cc_start: 0.7577 (mm) cc_final: 0.7115 (tt) REVERT: b 228 LYS cc_start: 0.8665 (ttpt) cc_final: 0.8265 (ttpt) REVERT: b 244 ILE cc_start: 0.9069 (mt) cc_final: 0.8428 (tp) REVERT: b 302 ARG cc_start: 0.8765 (ttm-80) cc_final: 0.8543 (ttm-80) REVERT: b 307 LEU cc_start: 0.8864 (mt) cc_final: 0.8482 (mt) REVERT: b 308 LEU cc_start: 0.8815 (mt) cc_final: 0.8528 (mm) REVERT: b 311 ARG cc_start: 0.8261 (ptt180) cc_final: 0.7678 (ptt-90) REVERT: b 317 MET cc_start: 0.8575 (tpp) cc_final: 0.8274 (tpp) REVERT: b 321 GLN cc_start: 0.7953 (tt0) cc_final: 0.7596 (tt0) REVERT: b 322 LEU cc_start: 0.8475 (tt) cc_final: 0.8267 (tt) REVERT: b 326 ILE cc_start: 0.7896 (mm) cc_final: 0.7630 (mm) REVERT: b 331 GLU cc_start: 0.7082 (mp0) cc_final: 0.6675 (mp0) REVERT: b 341 ARG cc_start: 0.8638 (ptt90) cc_final: 0.8219 (ptm-80) REVERT: b 346 ASN cc_start: 0.7201 (p0) cc_final: 0.6564 (p0) REVERT: b 352 ILE cc_start: 0.8656 (mm) cc_final: 0.8438 (mm) REVERT: b 355 GLN cc_start: 0.8678 (mt0) cc_final: 0.8429 (mt0) REVERT: b 386 LYS cc_start: 0.8530 (mtpt) cc_final: 0.8267 (mtpt) REVERT: b 391 GLU cc_start: 0.8236 (tp30) cc_final: 0.7992 (tp30) REVERT: b 417 ASP cc_start: 0.7903 (t0) cc_final: 0.7425 (t0) REVERT: b 629 LYS cc_start: 0.8383 (ttmt) cc_final: 0.7836 (ttmm) REVERT: b 640 PRO cc_start: 0.8537 (Cg_exo) cc_final: 0.8326 (Cg_endo) REVERT: m 29 CYS cc_start: 0.8536 (m) cc_final: 0.7879 (t) REVERT: m 36 GLN cc_start: 0.8391 (tp-100) cc_final: 0.8004 (tp-100) REVERT: m 44 ASN cc_start: 0.8363 (t0) cc_final: 0.7912 (t0) REVERT: m 71 GLN cc_start: 0.8301 (tp40) cc_final: 0.8022 (tp40) REVERT: m 72 THR cc_start: 0.8516 (p) cc_final: 0.8303 (p) REVERT: m 80 ILE cc_start: 0.8551 (mt) cc_final: 0.8247 (mm) REVERT: m 88 ASP cc_start: 0.8472 (m-30) cc_final: 0.8201 (m-30) REVERT: m 89 THR cc_start: 0.8889 (m) cc_final: 0.8651 (p) REVERT: m 108 ILE cc_start: 0.8906 (mt) cc_final: 0.8616 (mm) REVERT: m 116 MET cc_start: 0.7808 (mtm) cc_final: 0.7565 (mtm) REVERT: m 126 GLU cc_start: 0.8345 (tp30) cc_final: 0.7523 (tp30) REVERT: m 128 ASN cc_start: 0.8143 (m-40) cc_final: 0.7672 (m-40) REVERT: m 129 ILE cc_start: 0.8869 (mm) cc_final: 0.8637 (tp) REVERT: m 134 ILE cc_start: 0.8326 (mt) cc_final: 0.8105 (tp) REVERT: m 141 ARG cc_start: 0.8172 (mmt90) cc_final: 0.7795 (mmt90) REVERT: m 157 LEU cc_start: 0.8438 (mt) cc_final: 0.8183 (mt) REVERT: m 161 GLN cc_start: 0.8339 (tp40) cc_final: 0.8019 (tp-100) REVERT: m 180 TYR cc_start: 0.6936 (m-10) cc_final: 0.6665 (m-10) REVERT: m 186 GLU cc_start: 0.7483 (tt0) cc_final: 0.7254 (tt0) REVERT: m 209 CYS cc_start: 0.7302 (t) cc_final: 0.6455 (m) REVERT: m 220 LEU cc_start: 0.8096 (mm) cc_final: 0.7820 (mm) REVERT: m 225 PRO cc_start: 0.8902 (Cg_exo) cc_final: 0.8484 (Cg_endo) REVERT: m 228 LEU cc_start: 0.8807 (mt) cc_final: 0.8310 (pp) REVERT: m 234 HIS cc_start: 0.8120 (t-90) cc_final: 0.7661 (t-90) REVERT: m 240 LYS cc_start: 0.8511 (mttt) cc_final: 0.7781 (mmmm) REVERT: m 243 GLU cc_start: 0.8598 (tp30) cc_final: 0.8271 (tp30) REVERT: m 257 PHE cc_start: 0.8541 (p90) cc_final: 0.8218 (p90) REVERT: m 258 ARG cc_start: 0.8436 (mtm180) cc_final: 0.8066 (mtm180) REVERT: m 272 ILE cc_start: 0.8032 (mm) cc_final: 0.7633 (tp) REVERT: m 342 ASP cc_start: 0.7793 (t0) cc_final: 0.7414 (t0) REVERT: m 373 LEU cc_start: 0.7240 (tp) cc_final: 0.7038 (tt) REVERT: m 384 ILE cc_start: 0.8552 (tt) cc_final: 0.8314 (tt) REVERT: m 387 LEU cc_start: 0.8696 (tp) cc_final: 0.8165 (tp) REVERT: m 393 ASP cc_start: 0.7917 (t0) cc_final: 0.7563 (t0) REVERT: m 400 LYS cc_start: 0.8903 (mmtm) cc_final: 0.8635 (mmtt) REVERT: m 402 PHE cc_start: 0.7718 (m-80) cc_final: 0.7497 (m-10) REVERT: m 403 LYS cc_start: 0.7753 (mptt) cc_final: 0.7395 (mmtm) REVERT: m 407 TYR cc_start: 0.8656 (m-80) cc_final: 0.8096 (m-80) REVERT: m 414 PHE cc_start: 0.7818 (t80) cc_final: 0.7410 (t80) REVERT: c 30 LYS cc_start: 0.7845 (mtmm) cc_final: 0.7198 (mtmm) REVERT: c 44 THR cc_start: 0.9193 (m) cc_final: 0.8750 (p) REVERT: c 53 VAL cc_start: 0.8635 (t) cc_final: 0.8358 (m) REVERT: c 64 THR cc_start: 0.6484 (m) cc_final: 0.6146 (t) REVERT: c 68 VAL cc_start: 0.8240 (t) cc_final: 0.7910 (p) REVERT: c 78 TRP cc_start: 0.8306 (m-10) cc_final: 0.7473 (m-10) REVERT: c 82 PHE cc_start: 0.7995 (m-10) cc_final: 0.7413 (m-80) REVERT: c 84 ASN cc_start: 0.8485 (t0) cc_final: 0.7610 (t0) REVERT: c 86 GLN cc_start: 0.7963 (mm-40) cc_final: 0.6806 (mt0) REVERT: c 110 MET cc_start: 0.8419 (mmm) cc_final: 0.7870 (mmm) REVERT: c 115 GLU cc_start: 0.7952 (tt0) cc_final: 0.7588 (tt0) REVERT: c 134 MET cc_start: 0.7910 (mpp) cc_final: 0.7519 (mpp) REVERT: c 145 LEU cc_start: 0.8139 (mt) cc_final: 0.7878 (mt) REVERT: c 168 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7693 (mt-10) REVERT: c 171 ASP cc_start: 0.8100 (m-30) cc_final: 0.7696 (m-30) REVERT: y 415 GLN cc_start: 0.7771 (mm110) cc_final: 0.7357 (mm110) outliers start: 0 outliers final: 0 residues processed: 767 average time/residue: 0.3170 time to fit residues: 346.8142 Evaluate side-chains 752 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 752 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 78 optimal weight: 0.1980 chunk 187 optimal weight: 0.9990 chunk 189 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 127 optimal weight: 0.0570 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN ** M 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 231 ASN ** m 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.136924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.112457 restraints weight = 30885.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.116742 restraints weight = 16885.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.119720 restraints weight = 10578.322| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.5569 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= 0.147 Angle : 0.603 9.725 21822 Z= 0.311 Chirality : 0.045 0.164 2524 Planarity : 0.004 0.046 2752 Dihedral : 9.252 159.442 2154 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.06 % Allowed : 0.00 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.20), residues: 1954 helix: 1.31 (0.19), residues: 814 sheet: 0.34 (0.27), residues: 386 loop : 0.92 (0.26), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP c 172 HIS 0.004 0.001 HIS m 84 PHE 0.028 0.002 PHE m 121 TYR 0.023 0.002 TYR M 407 ARG 0.009 0.000 ARG C 97 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 815) hydrogen bonds : angle 4.96399 ( 2361) covalent geometry : bond 0.00298 (16108) covalent geometry : angle 0.60305 (21822) ********************** 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 769 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 768 time to evaluate : 1.657 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: 0.8089 (mttt) cc_final: 0.7610 (tptt) REVERT: B 44 ASN cc_start: 0.8691 (m-40) cc_final: 0.8387 (m-40) REVERT: B 45 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7135 (mm-30) REVERT: B 47 LEU cc_start: 0.8976 (mt) cc_final: 0.8541 (mt) REVERT: B 48 LYS cc_start: 0.9142 (mtmt) cc_final: 0.8489 (mttt) REVERT: B 49 GLN cc_start: 0.8595 (pt0) cc_final: 0.7804 (pp30) REVERT: B 50 MET cc_start: 0.8592 (mtm) cc_final: 0.7603 (mtm) REVERT: B 51 LEU cc_start: 0.8806 (mt) cc_final: 0.8433 (mt) REVERT: B 52 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7643 (mm-30) REVERT: B 54 ASN cc_start: 0.7987 (m110) cc_final: 0.7598 (m110) REVERT: B 59 LYS cc_start: 0.8799 (mtmm) cc_final: 0.8549 (mttt) REVERT: B 63 MET cc_start: 0.8587 (mmm) cc_final: 0.8006 (mmm) REVERT: B 74 LYS cc_start: 0.8865 (mmtt) cc_final: 0.8226 (mmtt) REVERT: B 80 PHE cc_start: 0.8632 (t80) cc_final: 0.8081 (t80) REVERT: B 85 LYS cc_start: 0.8584 (mttt) cc_final: 0.7761 (mttt) REVERT: B 90 LYS cc_start: 0.8530 (mttt) cc_final: 0.7755 (mmmm) REVERT: B 97 LEU cc_start: 0.8678 (mt) cc_final: 0.8201 (mm) REVERT: B 107 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7493 (mt-10) REVERT: B 112 LEU cc_start: 0.8409 (mp) cc_final: 0.7574 (mp) REVERT: B 125 LYS cc_start: 0.8923 (mttt) cc_final: 0.8461 (mtpp) REVERT: B 128 ASN cc_start: 0.8087 (t0) cc_final: 0.7749 (t0) REVERT: B 132 ARG cc_start: 0.8415 (mtm180) cc_final: 0.8100 (mtm-85) REVERT: B 137 ARG cc_start: 0.7803 (mtp-110) cc_final: 0.7283 (mtp-110) REVERT: B 147 ILE cc_start: 0.8293 (pt) cc_final: 0.7520 (pt) REVERT: B 148 VAL cc_start: 0.8837 (t) cc_final: 0.8346 (t) REVERT: B 151 MET cc_start: 0.7856 (mtp) cc_final: 0.7032 (mtp) REVERT: B 155 ILE cc_start: 0.9194 (mm) cc_final: 0.8870 (mm) REVERT: B 175 GLN cc_start: 0.8538 (tm-30) cc_final: 0.7777 (tm-30) REVERT: B 183 GLU cc_start: 0.8423 (mp0) cc_final: 0.8076 (mp0) REVERT: B 186 GLU cc_start: 0.8238 (pm20) cc_final: 0.7909 (pm20) REVERT: B 190 GLU cc_start: 0.8112 (tt0) cc_final: 0.7783 (tt0) REVERT: B 193 GLU cc_start: 0.8476 (tt0) cc_final: 0.8119 (tt0) REVERT: B 199 LYS cc_start: 0.8006 (mppt) cc_final: 0.7767 (mmtm) REVERT: B 202 LEU cc_start: 0.7514 (mm) cc_final: 0.7047 (tp) REVERT: B 213 GLU cc_start: 0.8288 (tt0) cc_final: 0.7688 (tt0) REVERT: B 221 LEU cc_start: 0.9194 (mt) cc_final: 0.8874 (pp) REVERT: B 228 LYS cc_start: 0.8698 (ttpt) cc_final: 0.8149 (ttpt) REVERT: B 246 HIS cc_start: 0.8386 (m-70) cc_final: 0.8146 (m-70) REVERT: B 247 MET cc_start: 0.7096 (tmm) cc_final: 0.6881 (tmm) REVERT: B 302 ARG cc_start: 0.8364 (mtt-85) cc_final: 0.7789 (ttm-80) REVERT: B 303 ASN cc_start: 0.8507 (m-40) cc_final: 0.8279 (t0) REVERT: B 307 LEU cc_start: 0.8706 (mm) cc_final: 0.8282 (tp) REVERT: B 308 LEU cc_start: 0.8642 (mt) cc_final: 0.8278 (mm) REVERT: B 311 ARG cc_start: 0.8068 (ptt180) cc_final: 0.7546 (ptt90) REVERT: B 317 MET cc_start: 0.8547 (tpp) cc_final: 0.8177 (tpp) REVERT: B 321 GLN cc_start: 0.8017 (tt0) cc_final: 0.7428 (tt0) REVERT: B 324 TRP cc_start: 0.8759 (t-100) cc_final: 0.8398 (t-100) REVERT: B 341 ARG cc_start: 0.8726 (ptt90) cc_final: 0.8252 (ptm-80) REVERT: B 346 ASN cc_start: 0.7140 (p0) cc_final: 0.6663 (p0) REVERT: B 348 GLU cc_start: 0.8137 (mp0) cc_final: 0.7799 (mp0) REVERT: B 360 MET cc_start: 0.8466 (tpp) cc_final: 0.7595 (tpp) REVERT: B 389 LYS cc_start: 0.8975 (mttt) cc_final: 0.8336 (ttmm) REVERT: B 391 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7584 (mt-10) REVERT: B 417 ASP cc_start: 0.8448 (m-30) cc_final: 0.8154 (m-30) REVERT: M 1 MET cc_start: 0.6947 (mpp) cc_final: 0.6447 (mpp) REVERT: M 17 GLU cc_start: 0.7573 (pt0) cc_final: 0.7057 (pt0) REVERT: M 21 LYS cc_start: 0.7807 (mttt) cc_final: 0.7012 (mttm) REVERT: M 29 CYS cc_start: 0.8687 (t) cc_final: 0.8241 (t) REVERT: M 31 TYR cc_start: 0.8268 (m-80) cc_final: 0.7840 (m-10) REVERT: M 34 GLU cc_start: 0.9010 (tt0) cc_final: 0.8637 (tt0) REVERT: M 41 ASP cc_start: 0.8537 (t0) cc_final: 0.8291 (t0) REVERT: M 43 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7519 (mt-10) REVERT: M 63 LYS cc_start: 0.8302 (mttt) cc_final: 0.7491 (tmtt) REVERT: M 78 PHE cc_start: 0.8750 (t80) cc_final: 0.8518 (t80) REVERT: M 89 THR cc_start: 0.9118 (m) cc_final: 0.8797 (p) REVERT: M 116 MET cc_start: 0.7966 (mtm) cc_final: 0.7598 (mtm) REVERT: M 119 ASN cc_start: 0.8201 (t0) cc_final: 0.7565 (t0) REVERT: M 126 GLU cc_start: 0.8280 (tp30) cc_final: 0.7603 (tp30) REVERT: M 128 ASN cc_start: 0.8235 (m-40) cc_final: 0.7896 (m110) REVERT: M 130 LEU cc_start: 0.8498 (tp) cc_final: 0.8162 (tp) REVERT: M 131 LYS cc_start: 0.8628 (mtmm) cc_final: 0.8195 (mttp) REVERT: M 135 LYS cc_start: 0.8884 (mmtt) cc_final: 0.8451 (mmtt) REVERT: M 157 LEU cc_start: 0.8465 (mt) cc_final: 0.8265 (pp) REVERT: M 161 GLN cc_start: 0.8382 (tp40) cc_final: 0.8078 (tp-100) REVERT: M 172 VAL cc_start: 0.8774 (t) cc_final: 0.8419 (t) REVERT: M 201 GLU cc_start: 0.5642 (tm-30) cc_final: 0.4742 (tm-30) REVERT: M 203 GLN cc_start: 0.7215 (mm110) cc_final: 0.6786 (mm-40) REVERT: M 209 CYS cc_start: 0.7291 (t) cc_final: 0.6454 (m) REVERT: M 220 LEU cc_start: 0.8244 (mm) cc_final: 0.7883 (mm) REVERT: M 234 HIS cc_start: 0.8126 (t-90) cc_final: 0.7771 (t-90) REVERT: M 242 TRP cc_start: 0.7890 (t-100) cc_final: 0.7170 (t-100) REVERT: M 245 GLU cc_start: 0.6726 (mm-30) cc_final: 0.6256 (mm-30) REVERT: M 257 PHE cc_start: 0.8449 (p90) cc_final: 0.8006 (p90) REVERT: M 258 ARG cc_start: 0.8349 (mtm180) cc_final: 0.7850 (mtm180) REVERT: M 262 TYR cc_start: 0.8365 (p90) cc_final: 0.8093 (p90) REVERT: M 298 LYS cc_start: 0.9024 (tttt) cc_final: 0.8605 (tttt) REVERT: M 393 ASP cc_start: 0.7784 (t0) cc_final: 0.7331 (t0) REVERT: M 400 LYS cc_start: 0.8948 (mmtm) cc_final: 0.8697 (mmtt) REVERT: M 402 PHE cc_start: 0.7649 (m-80) cc_final: 0.7260 (m-80) REVERT: M 414 PHE cc_start: 0.7786 (t80) cc_final: 0.7204 (t80) REVERT: C 23 VAL cc_start: 0.8784 (m) cc_final: 0.8278 (m) REVERT: C 44 THR cc_start: 0.9120 (m) cc_final: 0.8667 (p) REVERT: C 57 GLU cc_start: 0.7978 (tt0) cc_final: 0.7509 (tt0) REVERT: C 68 VAL cc_start: 0.8138 (t) cc_final: 0.7890 (p) REVERT: C 78 TRP cc_start: 0.8300 (m-10) cc_final: 0.7947 (m-10) REVERT: C 81 TYR cc_start: 0.7130 (m-80) cc_final: 0.6390 (m-80) REVERT: C 82 PHE cc_start: 0.7994 (m-10) cc_final: 0.7084 (m-80) REVERT: C 84 ASN cc_start: 0.8544 (t0) cc_final: 0.7842 (t0) REVERT: C 108 MET cc_start: 0.7746 (mtm) cc_final: 0.7511 (mtt) REVERT: C 110 MET cc_start: 0.8566 (mmm) cc_final: 0.8191 (mmm) REVERT: C 115 GLU cc_start: 0.7999 (tt0) cc_final: 0.7671 (tt0) REVERT: C 116 LEU cc_start: 0.7976 (mt) cc_final: 0.7735 (mt) REVERT: C 168 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7644 (mt-10) REVERT: C 171 ASP cc_start: 0.7890 (m-30) cc_final: 0.7672 (m-30) REVERT: C 176 GLN cc_start: 0.8753 (mt0) cc_final: 0.8096 (mp10) REVERT: C 178 ARG cc_start: 0.7514 (ttm110) cc_final: 0.6955 (ttm110) REVERT: b 43 LYS cc_start: 0.8203 (mttt) cc_final: 0.7674 (tptm) REVERT: b 47 LEU cc_start: 0.9073 (mt) cc_final: 0.8661 (mt) REVERT: b 50 MET cc_start: 0.8320 (mtm) cc_final: 0.7985 (mtm) REVERT: b 51 LEU cc_start: 0.8709 (tp) cc_final: 0.8489 (pp) REVERT: b 52 GLU cc_start: 0.8273 (mm-30) cc_final: 0.8050 (mm-30) REVERT: b 54 ASN cc_start: 0.8202 (m-40) cc_final: 0.7953 (m-40) REVERT: b 80 PHE cc_start: 0.8438 (t80) cc_final: 0.7989 (t80) REVERT: b 101 TYR cc_start: 0.8783 (t80) cc_final: 0.8542 (t80) REVERT: b 102 LEU cc_start: 0.8907 (mt) cc_final: 0.8704 (mt) REVERT: b 107 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7460 (mt-10) REVERT: b 112 LEU cc_start: 0.8272 (mp) cc_final: 0.7567 (mp) REVERT: b 121 GLN cc_start: 0.8080 (tt0) cc_final: 0.7731 (mt0) REVERT: b 124 LEU cc_start: 0.8897 (tp) cc_final: 0.8696 (tt) REVERT: b 132 ARG cc_start: 0.8340 (mtt180) cc_final: 0.8096 (mtm180) REVERT: b 137 ARG cc_start: 0.7888 (mtp85) cc_final: 0.7328 (mtp85) REVERT: b 139 LEU cc_start: 0.8650 (tt) cc_final: 0.8420 (tt) REVERT: b 142 ILE cc_start: 0.9109 (mm) cc_final: 0.8851 (mp) REVERT: b 147 ILE cc_start: 0.8415 (pt) cc_final: 0.7655 (pt) REVERT: b 150 ILE cc_start: 0.8284 (mt) cc_final: 0.7797 (mt) REVERT: b 151 MET cc_start: 0.7659 (mtp) cc_final: 0.6962 (mtp) REVERT: b 152 MET cc_start: 0.8018 (tpt) cc_final: 0.7768 (tpt) REVERT: b 162 LEU cc_start: 0.7886 (mt) cc_final: 0.7095 (tp) REVERT: b 190 GLU cc_start: 0.7961 (tt0) cc_final: 0.7663 (tt0) REVERT: b 199 LYS cc_start: 0.8022 (mppt) cc_final: 0.7777 (mmtm) REVERT: b 202 LEU cc_start: 0.7584 (mm) cc_final: 0.7143 (tt) REVERT: b 228 LYS cc_start: 0.8698 (ttpt) cc_final: 0.8297 (ttpt) REVERT: b 302 ARG cc_start: 0.8762 (ttm-80) cc_final: 0.8543 (ttm-80) REVERT: b 307 LEU cc_start: 0.8862 (mt) cc_final: 0.8499 (mt) REVERT: b 308 LEU cc_start: 0.8841 (mt) cc_final: 0.8537 (mm) REVERT: b 311 ARG cc_start: 0.8262 (ptt180) cc_final: 0.7731 (ptt-90) REVERT: b 317 MET cc_start: 0.8609 (tpp) cc_final: 0.8303 (tpp) REVERT: b 321 GLN cc_start: 0.8005 (tt0) cc_final: 0.7415 (tt0) REVERT: b 322 LEU cc_start: 0.8443 (tt) cc_final: 0.8217 (tt) REVERT: b 324 TRP cc_start: 0.8539 (t-100) cc_final: 0.8149 (t-100) REVERT: b 326 ILE cc_start: 0.7904 (mm) cc_final: 0.7649 (mm) REVERT: b 341 ARG cc_start: 0.8599 (ptt90) cc_final: 0.8199 (ptm-80) REVERT: b 346 ASN cc_start: 0.7208 (p0) cc_final: 0.6514 (p0) REVERT: b 352 ILE cc_start: 0.8633 (mm) cc_final: 0.8423 (mm) REVERT: b 355 GLN cc_start: 0.8686 (mt0) cc_final: 0.8434 (mt0) REVERT: b 360 MET cc_start: 0.8022 (tpp) cc_final: 0.7062 (tpp) REVERT: b 386 LYS cc_start: 0.8581 (mtpt) cc_final: 0.8306 (mtpt) REVERT: b 391 GLU cc_start: 0.8251 (tp30) cc_final: 0.8014 (tp30) REVERT: b 417 ASP cc_start: 0.7935 (t0) cc_final: 0.7445 (t0) REVERT: b 629 LYS cc_start: 0.8390 (ttmt) cc_final: 0.7833 (ttmm) REVERT: b 631 THR cc_start: 0.8976 (m) cc_final: 0.8747 (t) REVERT: b 640 PRO cc_start: 0.8558 (Cg_exo) cc_final: 0.8353 (Cg_endo) REVERT: m 21 LYS cc_start: 0.7995 (mttt) cc_final: 0.7489 (mttm) REVERT: m 29 CYS cc_start: 0.8510 (m) cc_final: 0.7879 (t) REVERT: m 36 GLN cc_start: 0.8363 (tp-100) cc_final: 0.7982 (tp-100) REVERT: m 45 VAL cc_start: 0.8872 (t) cc_final: 0.8652 (t) REVERT: m 63 LYS cc_start: 0.8465 (mttt) cc_final: 0.7650 (tmtt) REVERT: m 71 GLN cc_start: 0.8305 (tp40) cc_final: 0.7880 (tp40) REVERT: m 72 THR cc_start: 0.8525 (p) cc_final: 0.8288 (p) REVERT: m 80 ILE cc_start: 0.8598 (mt) cc_final: 0.8282 (mm) REVERT: m 89 THR cc_start: 0.8888 (m) cc_final: 0.8604 (p) REVERT: m 108 ILE cc_start: 0.8907 (mt) cc_final: 0.8621 (mm) REVERT: m 116 MET cc_start: 0.7790 (mtm) cc_final: 0.7477 (mtm) REVERT: m 126 GLU cc_start: 0.8329 (tp30) cc_final: 0.7525 (tp30) REVERT: m 128 ASN cc_start: 0.8089 (m-40) cc_final: 0.7701 (m-40) REVERT: m 134 ILE cc_start: 0.8166 (mt) cc_final: 0.7799 (tt) REVERT: m 140 LEU cc_start: 0.8489 (mt) cc_final: 0.8207 (tt) REVERT: m 141 ARG cc_start: 0.8160 (mmt90) cc_final: 0.7733 (mmt90) REVERT: m 157 LEU cc_start: 0.8457 (mt) cc_final: 0.8162 (mt) REVERT: m 161 GLN cc_start: 0.8337 (tp40) cc_final: 0.8021 (tp-100) REVERT: m 180 TYR cc_start: 0.6961 (m-10) cc_final: 0.6652 (m-10) REVERT: m 186 GLU cc_start: 0.7469 (tt0) cc_final: 0.7243 (tt0) REVERT: m 209 CYS cc_start: 0.7362 (t) cc_final: 0.6492 (m) REVERT: m 220 LEU cc_start: 0.8098 (mm) cc_final: 0.7867 (mm) REVERT: m 225 PRO cc_start: 0.8918 (Cg_exo) cc_final: 0.8436 (Cg_endo) REVERT: m 228 LEU cc_start: 0.8799 (mt) cc_final: 0.8308 (pp) REVERT: m 240 LYS cc_start: 0.8533 (mttt) cc_final: 0.7747 (mmmm) REVERT: m 243 GLU cc_start: 0.8609 (tp30) cc_final: 0.8297 (tp30) REVERT: m 257 PHE cc_start: 0.8545 (p90) cc_final: 0.8246 (p90) REVERT: m 258 ARG cc_start: 0.8464 (mtm180) cc_final: 0.8144 (mtm180) REVERT: m 262 TYR cc_start: 0.8179 (p90) cc_final: 0.6999 (p90) REVERT: m 272 ILE cc_start: 0.8080 (mm) cc_final: 0.7698 (tp) REVERT: m 373 LEU cc_start: 0.7377 (tp) cc_final: 0.7145 (tt) REVERT: m 378 LYS cc_start: 0.7949 (ptmm) cc_final: 0.7636 (ptmm) REVERT: m 384 ILE cc_start: 0.8597 (tt) cc_final: 0.8328 (tt) REVERT: m 387 LEU cc_start: 0.8698 (tp) cc_final: 0.8263 (tp) REVERT: m 393 ASP cc_start: 0.7912 (t0) cc_final: 0.7448 (t0) REVERT: m 402 PHE cc_start: 0.7707 (m-80) cc_final: 0.7441 (m-10) REVERT: m 403 LYS cc_start: 0.7757 (mptt) cc_final: 0.7443 (mmtt) REVERT: m 407 TYR cc_start: 0.8633 (m-80) cc_final: 0.8137 (m-80) REVERT: m 414 PHE cc_start: 0.7771 (t80) cc_final: 0.7374 (t80) REVERT: c 30 LYS cc_start: 0.7888 (mtmm) cc_final: 0.7277 (mtmm) REVERT: c 39 LEU cc_start: 0.8326 (mt) cc_final: 0.8119 (mt) REVERT: c 44 THR cc_start: 0.9191 (m) cc_final: 0.8725 (p) REVERT: c 53 VAL cc_start: 0.8671 (t) cc_final: 0.8362 (m) REVERT: c 64 THR cc_start: 0.6420 (m) cc_final: 0.6108 (t) REVERT: c 68 VAL cc_start: 0.8227 (t) cc_final: 0.7886 (p) REVERT: c 78 TRP cc_start: 0.8323 (m-10) cc_final: 0.7408 (m-10) REVERT: c 84 ASN cc_start: 0.8559 (t0) cc_final: 0.7756 (t0) REVERT: c 110 MET cc_start: 0.8382 (mmm) cc_final: 0.7901 (mmm) REVERT: c 115 GLU cc_start: 0.7920 (tt0) cc_final: 0.7518 (tt0) REVERT: c 116 LEU cc_start: 0.7956 (mt) cc_final: 0.7693 (mt) REVERT: c 134 MET cc_start: 0.7973 (mpp) cc_final: 0.7598 (mpp) REVERT: c 171 ASP cc_start: 0.7983 (m-30) cc_final: 0.7562 (m-30) REVERT: y 415 GLN cc_start: 0.7776 (mm110) cc_final: 0.7360 (mm110) outliers start: 1 outliers final: 0 residues processed: 768 average time/residue: 0.3316 time to fit residues: 367.3842 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 : 1.632 ------------------------------------------------------------------------------- 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: 0.4980 chunk 60 optimal weight: 0.1980 chunk 47 optimal weight: 0.7980 chunk 3 optimal weight: 0.2980 chunk 7 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 4 optimal weight: 0.0050 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN B 355 GLN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS b 231 ASN m 44 ASN m 53 HIS ** m 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 95 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.137823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.113613 restraints weight = 30602.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.117964 restraints weight = 16878.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.120977 restraints weight = 10652.998| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.5751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16108 Z= 0.112 Angle : 0.580 9.084 21822 Z= 0.297 Chirality : 0.045 0.166 2524 Planarity : 0.004 0.046 2752 Dihedral : 8.908 156.333 2154 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.20), residues: 1954 helix: 1.36 (0.19), residues: 814 sheet: 0.37 (0.27), residues: 386 loop : 0.97 (0.26), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.003 TRP c 172 HIS 0.004 0.001 HIS m 84 PHE 0.018 0.001 PHE C 51 TYR 0.019 0.001 TYR M 407 ARG 0.007 0.000 ARG b 218 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 815) hydrogen bonds : angle 4.79323 ( 2361) covalent geometry : bond 0.00235 (16108) covalent geometry : angle 0.58037 (21822) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7065.28 seconds wall clock time: 122 minutes 24.24 seconds (7344.24 seconds total)