Starting phenix.real_space_refine on Tue Jan 13 22:37:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tr2_26079/01_2026/7tr2_26079.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tr2_26079/01_2026/7tr2_26079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tr2_26079/01_2026/7tr2_26079.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tr2_26079/01_2026/7tr2_26079.map" model { file = "/net/cci-nas-00/data/ceres_data/7tr2_26079/01_2026/7tr2_26079.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tr2_26079/01_2026/7tr2_26079.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.002 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 5 5.49 5 Mg 1 5.21 5 S 62 5.16 5 C 5998 2.51 5 N 1654 2.21 5 O 1866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9586 Number of models: 1 Model: "" Number of chains: 6 Chain: "K" Number of atoms: 2650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2650 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 10, 'TRANS': 327} Chain breaks: 1 Chain: "A" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3437 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain: "B" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3376 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 20, 'TRANS': 408} Chain: "A" 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} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.27, per 1000 atoms: 0.24 Number of scatterers: 9586 At special positions: 0 Unit cell: (109.521, 72.165, 112.917, 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 62 16.00 P 5 15.00 Mg 1 11.99 O 1866 8.00 N 1654 7.00 C 5998 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: 0.92 Conformation dependent library (CDL) restraints added in 585.5 milliseconds 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2250 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 10 sheets defined 49.7% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'K' and resid 36 through 51 removed outlier: 4.309A pdb=" N LYS K 45 " --> pdb=" O ASN K 41 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ILE K 46 " --> pdb=" O ARG K 42 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP K 47 " --> pdb=" O LEU K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 166 Processing helix chain 'K' and resid 166 through 176 removed outlier: 3.807A pdb=" N LEU K 170 " --> pdb=" O THR K 166 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP K 171 " --> pdb=" O GLN K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 196 Processing helix chain 'K' and resid 203 through 220 Processing helix chain 'K' and resid 274 through 289 Processing helix chain 'K' and resid 347 through 372 removed outlier: 3.582A pdb=" N ASN K 351 " --> pdb=" O GLY K 347 " (cutoff:3.500A) Processing helix chain 'K' and resid 373 through 378 removed outlier: 4.421A pdb=" N ASN K 377 " --> pdb=" O ARG K 374 " (cutoff:3.500A) Processing helix chain 'K' and resid 380 through 383 removed outlier: 3.706A pdb=" N ASP K 383 " --> pdb=" O PRO K 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 380 through 383' Processing helix chain 'K' and resid 384 through 390 Processing helix chain 'K' and resid 412 through 427 removed outlier: 3.962A pdb=" N ALA K 426 " --> pdb=" O TYR K 422 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS K 427 " --> pdb=" O ALA K 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 36 through 42 removed outlier: 4.120A pdb=" N LYS A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 removed outlier: 3.782A pdb=" N GLU A 113 " --> pdb=" O ILE A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 110 through 113' Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.236A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.528A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.675A pdb=" N ILE A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 239 removed outlier: 3.688A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 243 Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.167A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.840A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.971A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.837A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 436 removed outlier: 3.679A pdb=" N GLY A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 40 through 46 removed outlier: 4.297A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 69 through 78 removed outlier: 4.621A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.566A pdb=" N PHE B 85 " --> pdb=" O GLY B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 126 removed outlier: 3.769A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 180 through 193 removed outlier: 3.741A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.651A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 4.216A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.983A pdb=" N MET B 299 " --> pdb=" O SER B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 373 through 390 removed outlier: 4.143A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 removed outlier: 4.097A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU B 401 " --> pdb=" O TRP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.633A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN B 426 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 150 through 152 removed outlier: 8.970A pdb=" N ARG K 150 " --> pdb=" O ILE K 26 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL K 28 " --> pdb=" O ARG K 150 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE K 152 " --> pdb=" O VAL K 28 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL K 30 " --> pdb=" O PHE K 152 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR K 180 " --> pdb=" O VAL K 401 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE K 403 " --> pdb=" O THR K 180 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE K 182 " --> pdb=" O ILE K 403 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N CYS K 405 " --> pdb=" O PHE K 182 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR K 184 " --> pdb=" O CYS K 405 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA K 179 " --> pdb=" O SER K 330 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ILE K 332 " --> pdb=" O ALA K 179 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL K 181 " --> pdb=" O ILE K 332 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 113 through 114 Processing sheet with id=AA3, first strand: chain 'K' and resid 291 through 294 removed outlier: 6.442A pdb=" N SER K 292 " --> pdb=" O THR K 299 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N THR K 299 " --> pdb=" O SER K 292 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 93 removed outlier: 8.515A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA6, first strand: chain 'A' and resid 269 through 272 Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.271A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 163 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS B 137 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N MET B 164 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.271A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 163 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS B 137 " --> pdb=" O PHE B 167 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AB1, first strand: chain 'B' and resid 244 through 246 removed outlier: 3.554A pdb=" N LEU B 246 " --> pdb=" O VAL B 353 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1341 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: 1.75 Time building geometry restraints manager: 1.17 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: 1705 1.32 - 1.45: 2519 1.45 - 1.57: 5446 1.57 - 1.69: 13 1.69 - 1.82: 96 Bond restraints: 9779 Sorted by residual: bond pdb=" N GLU K 338 " pdb=" CA GLU K 338 " ideal model delta sigma weight residual 1.455 1.493 -0.037 1.23e-02 6.61e+03 9.11e+00 bond pdb=" N ARG K 339 " pdb=" CA ARG K 339 " ideal model delta sigma weight residual 1.455 1.486 -0.030 1.21e-02 6.83e+03 6.33e+00 bond pdb=" N SER K 337 " pdb=" CA SER K 337 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.37e-02 5.33e+03 6.05e+00 bond pdb=" N GLU A 220 " pdb=" CA GLU A 220 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.28e-02 6.10e+03 5.99e+00 bond pdb=" N GLU A 254 " pdb=" CA GLU A 254 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.57e+00 ... (remaining 9774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 12799 1.77 - 3.55: 345 3.55 - 5.32: 103 5.32 - 7.10: 23 7.10 - 8.87: 3 Bond angle restraints: 13273 Sorted by residual: angle pdb=" CA GLU A 417 " pdb=" CB GLU A 417 " pdb=" CG GLU A 417 " ideal model delta sigma weight residual 114.10 122.17 -8.07 2.00e+00 2.50e-01 1.63e+01 angle pdb=" CG LYS B 336 " pdb=" CD LYS B 336 " pdb=" CE LYS B 336 " ideal model delta sigma weight residual 111.30 120.17 -8.87 2.30e+00 1.89e-01 1.49e+01 angle pdb=" CB GLU A 417 " pdb=" CG GLU A 417 " pdb=" CD GLU A 417 " ideal model delta sigma weight residual 112.60 119.13 -6.53 1.70e+00 3.46e-01 1.47e+01 angle pdb=" CB GLN K 280 " pdb=" CG GLN K 280 " pdb=" CD GLN K 280 " ideal model delta sigma weight residual 112.60 118.60 -6.00 1.70e+00 3.46e-01 1.24e+01 angle pdb=" CA GLU A 434 " pdb=" CB GLU A 434 " pdb=" CG GLU A 434 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 ... (remaining 13268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.34: 5666 29.34 - 58.67: 244 58.67 - 88.01: 35 88.01 - 117.35: 5 117.35 - 146.68: 11 Dihedral angle restraints: 5961 sinusoidal: 2465 harmonic: 3496 Sorted by residual: dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -32.99 137.58 1 2.00e+01 2.50e-03 4.17e+01 dihedral pdb=" CA ALA B 54 " pdb=" C ALA B 54 " pdb=" N THR B 55 " pdb=" CA THR B 55 " ideal model delta harmonic sigma weight residual -180.00 -154.00 -26.00 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 155.29 -86.02 1 2.00e+01 2.50e-03 2.23e+01 ... (remaining 5958 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 837 0.030 - 0.060: 427 0.060 - 0.090: 114 0.090 - 0.119: 72 0.119 - 0.149: 32 Chirality restraints: 1482 Sorted by residual: chirality pdb=" CA VAL A 204 " pdb=" N VAL A 204 " pdb=" C VAL A 204 " pdb=" CB VAL A 204 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CA ILE K 309 " pdb=" N ILE K 309 " pdb=" C ILE K 309 " pdb=" CB ILE K 309 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA VAL B 60 " pdb=" N VAL B 60 " pdb=" C VAL B 60 " pdb=" CB VAL B 60 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.41e-01 ... (remaining 1479 not shown) Planarity restraints: 1725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN K 280 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.33e+01 pdb=" CD GLN K 280 " -0.063 2.00e-02 2.50e+03 pdb=" OE1 GLN K 280 " 0.023 2.00e-02 2.50e+03 pdb=" NE2 GLN K 280 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 388 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C TRP A 388 " 0.039 2.00e-02 2.50e+03 pdb=" O TRP A 388 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA A 389 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 390 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.38e+00 pdb=" C ARG A 390 " -0.036 2.00e-02 2.50e+03 pdb=" O ARG A 390 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 391 " 0.012 2.00e-02 2.50e+03 ... (remaining 1722 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 45 2.53 - 3.12: 7254 3.12 - 3.71: 14599 3.71 - 4.31: 20154 4.31 - 4.90: 35312 Nonbonded interactions: 77364 Sorted by model distance: nonbonded pdb=" O3G GTP A 501 " pdb="MG MG A 502 " model vdw 1.933 2.170 nonbonded pdb=" OG SER B 172 " pdb=" OD1 ASP B 203 " model vdw 2.054 3.040 nonbonded pdb=" OG1 THR K 157 " pdb=" OE1 GLN K 160 " model vdw 2.116 3.040 nonbonded pdb=" OG SER K 409 " pdb=" OE1 GLN K 411 " model vdw 2.134 3.040 nonbonded pdb=" OG SER A 48 " pdb=" O ARG A 243 " model vdw 2.145 3.040 ... (remaining 77359 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.690 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.200 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:8.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9779 Z= 0.207 Angle : 0.778 8.872 13273 Z= 0.400 Chirality : 0.044 0.149 1482 Planarity : 0.005 0.068 1725 Dihedral : 18.071 146.684 3711 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.05 % Allowed : 16.97 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.24), residues: 1199 helix: 1.42 (0.23), residues: 496 sheet: -0.35 (0.38), residues: 194 loop : -1.05 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 320 TYR 0.020 0.001 TYR A 172 PHE 0.030 0.001 PHE K 152 TRP 0.010 0.001 TRP A 21 HIS 0.004 0.001 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 9779) covalent geometry : angle 0.77781 (13273) hydrogen bonds : bond 0.14696 ( 455) hydrogen bonds : angle 5.92379 ( 1341) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 176 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: K 39 GLU cc_start: 0.7952 (mp0) cc_final: 0.7373 (pt0) REVERT: K 162 TYR cc_start: 0.7410 (t80) cc_final: 0.6714 (t80) REVERT: K 420 LEU cc_start: 0.9183 (mt) cc_final: 0.8931 (mp) REVERT: A 326 LYS cc_start: 0.6104 (ptpt) cc_final: 0.5833 (ptpt) REVERT: B 57 ASN cc_start: 0.7588 (t0) cc_final: 0.7191 (t0) REVERT: B 163 ILE cc_start: 0.9349 (tp) cc_final: 0.9056 (tp) REVERT: B 236 VAL cc_start: 0.9261 (t) cc_final: 0.8932 (p) outliers start: 11 outliers final: 3 residues processed: 183 average time/residue: 0.5657 time to fit residues: 110.7733 Evaluate side-chains 171 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 168 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 27 SER Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain B residue 135 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 273 ASN A 61 HIS A 206 ASN A 256 GLN B 131 GLN B 204 ASN B 279 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.110397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.085797 restraints weight = 15090.562| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.39 r_work: 0.3038 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9779 Z= 0.242 Angle : 0.647 9.629 13273 Z= 0.318 Chirality : 0.046 0.209 1482 Planarity : 0.004 0.041 1725 Dihedral : 12.283 137.643 1450 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.68 % Allowed : 14.96 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.25), residues: 1199 helix: 1.75 (0.24), residues: 501 sheet: -0.27 (0.35), residues: 220 loop : -0.86 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 221 TYR 0.014 0.001 TYR K 213 PHE 0.015 0.001 PHE A 149 TRP 0.012 0.002 TRP A 21 HIS 0.004 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00581 ( 9779) covalent geometry : angle 0.64713 (13273) hydrogen bonds : bond 0.04889 ( 455) hydrogen bonds : angle 4.38448 ( 1341) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.380 Fit side-chains REVERT: K 39 GLU cc_start: 0.8107 (mp0) cc_final: 0.7660 (pt0) REVERT: K 113 MET cc_start: 0.7778 (tmm) cc_final: 0.7511 (tmm) REVERT: K 233 GLU cc_start: 0.8299 (tt0) cc_final: 0.8061 (tt0) REVERT: K 284 GLU cc_start: 0.8419 (tp30) cc_final: 0.8002 (tp30) REVERT: K 420 LEU cc_start: 0.9143 (mt) cc_final: 0.8922 (mp) REVERT: A 327 ASP cc_start: 0.8341 (m-30) cc_final: 0.8116 (p0) REVERT: B 57 ASN cc_start: 0.8009 (t0) cc_final: 0.7485 (t0) REVERT: B 163 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.9023 (tp) outliers start: 28 outliers final: 10 residues processed: 202 average time/residue: 0.5694 time to fit residues: 123.2845 Evaluate side-chains 180 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 169 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain K residue 162 TYR Chi-restraints excluded: chain K residue 209 MET Chi-restraints excluded: chain K residue 291 CYS Chi-restraints excluded: chain K residue 303 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 163 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 112 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 117 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 HIS ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.111759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.086795 restraints weight = 15055.860| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.44 r_work: 0.3054 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9779 Z= 0.174 Angle : 0.591 8.303 13273 Z= 0.292 Chirality : 0.046 0.469 1482 Planarity : 0.004 0.039 1725 Dihedral : 8.086 137.423 1446 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.59 % Allowed : 16.11 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.25), residues: 1199 helix: 1.92 (0.24), residues: 499 sheet: -0.06 (0.35), residues: 219 loop : -0.81 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 221 TYR 0.012 0.001 TYR K 213 PHE 0.014 0.001 PHE A 149 TRP 0.012 0.001 TRP A 21 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 9779) covalent geometry : angle 0.59131 (13273) hydrogen bonds : bond 0.04178 ( 455) hydrogen bonds : angle 4.13145 ( 1341) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: K 39 GLU cc_start: 0.8153 (mp0) cc_final: 0.7719 (pt0) REVERT: K 103 ARG cc_start: 0.8458 (mmm-85) cc_final: 0.7846 (mmt180) REVERT: K 113 MET cc_start: 0.7642 (tmm) cc_final: 0.7316 (tmt) REVERT: K 162 TYR cc_start: 0.7102 (t80) cc_final: 0.6678 (t80) REVERT: K 420 LEU cc_start: 0.9136 (mt) cc_final: 0.8929 (mp) REVERT: A 73 THR cc_start: 0.8350 (m) cc_final: 0.8125 (p) REVERT: A 112 LYS cc_start: 0.8969 (mttm) cc_final: 0.8684 (mttm) REVERT: A 302 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8487 (mtm) REVERT: A 392 ASP cc_start: 0.8459 (t0) cc_final: 0.8167 (t70) REVERT: A 396 ASP cc_start: 0.8727 (m-30) cc_final: 0.8294 (m-30) REVERT: A 417 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7623 (tm-30) REVERT: A 422 ARG cc_start: 0.8494 (tpt90) cc_final: 0.8260 (tpt90) REVERT: B 57 ASN cc_start: 0.8101 (t0) cc_final: 0.7565 (t0) REVERT: B 306 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8693 (mtm110) outliers start: 27 outliers final: 7 residues processed: 200 average time/residue: 0.5931 time to fit residues: 127.0623 Evaluate side-chains 181 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 172 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 303 SER Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 403 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 10 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 115 optimal weight: 0.0980 chunk 53 optimal weight: 5.9990 chunk 96 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 273 ASN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN B 416 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.112454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.087571 restraints weight = 15054.144| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.43 r_work: 0.3070 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9779 Z= 0.139 Angle : 0.562 7.266 13273 Z= 0.276 Chirality : 0.044 0.348 1482 Planarity : 0.004 0.042 1725 Dihedral : 7.208 135.503 1446 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.16 % Allowed : 17.93 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.25), residues: 1199 helix: 2.02 (0.24), residues: 504 sheet: 0.02 (0.36), residues: 211 loop : -0.79 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 221 TYR 0.011 0.001 TYR B 159 PHE 0.013 0.001 PHE A 149 TRP 0.012 0.001 TRP A 21 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9779) covalent geometry : angle 0.56246 (13273) hydrogen bonds : bond 0.03819 ( 455) hydrogen bonds : angle 4.05013 ( 1341) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: K 39 GLU cc_start: 0.8161 (mp0) cc_final: 0.7703 (pt0) REVERT: K 103 ARG cc_start: 0.8496 (mmm-85) cc_final: 0.8272 (mmm-85) REVERT: K 113 MET cc_start: 0.7700 (tmm) cc_final: 0.7352 (tmt) REVERT: K 160 GLN cc_start: 0.7609 (pm20) cc_final: 0.7406 (pm20) REVERT: K 356 ILE cc_start: 0.8912 (mt) cc_final: 0.8693 (mp) REVERT: K 420 LEU cc_start: 0.9135 (mt) cc_final: 0.8914 (mp) REVERT: A 392 ASP cc_start: 0.8534 (t0) cc_final: 0.8134 (t70) REVERT: A 396 ASP cc_start: 0.8728 (m-30) cc_final: 0.8264 (m-30) REVERT: A 432 TYR cc_start: 0.9030 (OUTLIER) cc_final: 0.8052 (t80) REVERT: B 57 ASN cc_start: 0.8104 (t0) cc_final: 0.7564 (t0) REVERT: B 236 VAL cc_start: 0.9151 (t) cc_final: 0.8803 (p) outliers start: 33 outliers final: 13 residues processed: 202 average time/residue: 0.5819 time to fit residues: 126.0564 Evaluate side-chains 183 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 412 HIS Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 403 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 105 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 418 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.109804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.085293 restraints weight = 15167.241| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.38 r_work: 0.3029 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9779 Z= 0.226 Angle : 0.618 8.416 13273 Z= 0.304 Chirality : 0.046 0.269 1482 Planarity : 0.005 0.092 1725 Dihedral : 7.229 138.079 1446 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.36 % Allowed : 19.56 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.25), residues: 1199 helix: 2.02 (0.24), residues: 498 sheet: 0.03 (0.35), residues: 220 loop : -0.84 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 221 TYR 0.016 0.002 TYR A 24 PHE 0.016 0.001 PHE A 149 TRP 0.011 0.001 TRP A 21 HIS 0.004 0.001 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00544 ( 9779) covalent geometry : angle 0.61797 (13273) hydrogen bonds : bond 0.04442 ( 455) hydrogen bonds : angle 4.15245 ( 1341) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.389 Fit side-chains REVERT: K 39 GLU cc_start: 0.8166 (mp0) cc_final: 0.7739 (pt0) REVERT: K 103 ARG cc_start: 0.8554 (mmm-85) cc_final: 0.8038 (mmt180) REVERT: K 113 MET cc_start: 0.7683 (tmm) cc_final: 0.7322 (tmt) REVERT: K 420 LEU cc_start: 0.9161 (mt) cc_final: 0.8923 (mp) REVERT: A 165 SER cc_start: 0.8911 (m) cc_final: 0.8689 (p) REVERT: A 392 ASP cc_start: 0.8621 (t0) cc_final: 0.8346 (t70) REVERT: A 432 TYR cc_start: 0.9087 (OUTLIER) cc_final: 0.8036 (t80) REVERT: B 57 ASN cc_start: 0.8156 (t0) cc_final: 0.7604 (t0) REVERT: B 306 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8530 (mtm110) outliers start: 35 outliers final: 22 residues processed: 195 average time/residue: 0.5735 time to fit residues: 120.0778 Evaluate side-chains 195 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain K residue 162 TYR Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 412 HIS Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 403 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 84 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 273 ASN K 378 HIS ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS B 279 GLN B 416 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.111819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.087012 restraints weight = 15002.173| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.44 r_work: 0.3061 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9779 Z= 0.138 Angle : 0.584 8.959 13273 Z= 0.284 Chirality : 0.044 0.240 1482 Planarity : 0.004 0.065 1725 Dihedral : 7.047 136.414 1446 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.97 % Allowed : 20.81 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.25), residues: 1199 helix: 2.10 (0.24), residues: 497 sheet: 0.03 (0.36), residues: 214 loop : -0.79 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 221 TYR 0.019 0.001 TYR A 103 PHE 0.013 0.001 PHE A 149 TRP 0.012 0.001 TRP A 21 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9779) covalent geometry : angle 0.58418 (13273) hydrogen bonds : bond 0.03804 ( 455) hydrogen bonds : angle 4.04689 ( 1341) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 0.430 Fit side-chains REVERT: K 39 GLU cc_start: 0.8151 (mp0) cc_final: 0.7729 (pt0) REVERT: K 103 ARG cc_start: 0.8536 (mmm-85) cc_final: 0.8245 (mmm-85) REVERT: K 113 MET cc_start: 0.7753 (tmm) cc_final: 0.7436 (tmt) REVERT: K 233 GLU cc_start: 0.8267 (tt0) cc_final: 0.8046 (tt0) REVERT: K 356 ILE cc_start: 0.8907 (mt) cc_final: 0.8694 (mp) REVERT: K 420 LEU cc_start: 0.9128 (mt) cc_final: 0.8882 (mp) REVERT: A 165 SER cc_start: 0.8896 (m) cc_final: 0.8674 (p) REVERT: A 432 TYR cc_start: 0.9021 (OUTLIER) cc_final: 0.8115 (t80) REVERT: B 57 ASN cc_start: 0.8105 (t0) cc_final: 0.7558 (t0) REVERT: B 306 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8495 (mtm110) outliers start: 31 outliers final: 18 residues processed: 195 average time/residue: 0.5472 time to fit residues: 115.0700 Evaluate side-chains 194 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain K residue 162 TYR Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 412 HIS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 380 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 10 optimal weight: 0.0970 chunk 103 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.112364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.087634 restraints weight = 15014.702| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.43 r_work: 0.3070 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9779 Z= 0.132 Angle : 0.577 8.783 13273 Z= 0.282 Chirality : 0.043 0.228 1482 Planarity : 0.004 0.050 1725 Dihedral : 6.859 133.796 1446 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.68 % Allowed : 21.76 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.25), residues: 1199 helix: 2.11 (0.24), residues: 498 sheet: 0.16 (0.36), residues: 219 loop : -0.78 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 221 TYR 0.020 0.001 TYR A 103 PHE 0.013 0.001 PHE A 149 TRP 0.012 0.001 TRP A 21 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9779) covalent geometry : angle 0.57730 (13273) hydrogen bonds : bond 0.03673 ( 455) hydrogen bonds : angle 4.00315 ( 1341) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.405 Fit side-chains REVERT: K 39 GLU cc_start: 0.8164 (mp0) cc_final: 0.7735 (pt0) REVERT: K 103 ARG cc_start: 0.8506 (mmm-85) cc_final: 0.8232 (mmm-85) REVERT: K 113 MET cc_start: 0.7752 (tmm) cc_final: 0.7469 (tmt) REVERT: K 146 PHE cc_start: 0.8146 (m-80) cc_final: 0.7707 (m-10) REVERT: K 160 GLN cc_start: 0.7608 (pm20) cc_final: 0.7354 (pm20) REVERT: K 233 GLU cc_start: 0.8272 (tt0) cc_final: 0.8043 (tt0) REVERT: K 356 ILE cc_start: 0.8889 (mt) cc_final: 0.8675 (mp) REVERT: K 420 LEU cc_start: 0.9110 (mt) cc_final: 0.8839 (mp) REVERT: A 165 SER cc_start: 0.8892 (m) cc_final: 0.8684 (p) REVERT: A 198 SER cc_start: 0.8848 (m) cc_final: 0.8570 (p) REVERT: A 377 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8127 (ttm) REVERT: A 392 ASP cc_start: 0.8416 (t70) cc_final: 0.8056 (t0) REVERT: A 432 TYR cc_start: 0.9010 (OUTLIER) cc_final: 0.8119 (t80) REVERT: B 57 ASN cc_start: 0.8135 (t0) cc_final: 0.7612 (t0) REVERT: B 236 VAL cc_start: 0.9115 (t) cc_final: 0.8767 (p) REVERT: B 297 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8633 (mtpt) REVERT: B 306 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8414 (mtm110) outliers start: 28 outliers final: 18 residues processed: 194 average time/residue: 0.5404 time to fit residues: 112.8981 Evaluate side-chains 197 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain K residue 162 TYR Chi-restraints excluded: chain K residue 412 HIS Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 339 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS B 416 ASN ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.108994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.084609 restraints weight = 15245.034| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.39 r_work: 0.3015 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9779 Z= 0.258 Angle : 0.661 8.923 13273 Z= 0.325 Chirality : 0.046 0.234 1482 Planarity : 0.004 0.050 1725 Dihedral : 7.003 136.735 1446 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.16 % Allowed : 21.38 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.25), residues: 1199 helix: 1.96 (0.24), residues: 498 sheet: 0.17 (0.36), residues: 214 loop : -0.88 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 221 TYR 0.022 0.002 TYR A 103 PHE 0.013 0.002 PHE A 149 TRP 0.009 0.001 TRP A 21 HIS 0.005 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00624 ( 9779) covalent geometry : angle 0.66083 (13273) hydrogen bonds : bond 0.04611 ( 455) hydrogen bonds : angle 4.21314 ( 1341) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 0.430 Fit side-chains REVERT: K 39 GLU cc_start: 0.8161 (mp0) cc_final: 0.7786 (pt0) REVERT: K 103 ARG cc_start: 0.8600 (mmm-85) cc_final: 0.8155 (mmt180) REVERT: K 113 MET cc_start: 0.7792 (tmm) cc_final: 0.7455 (tmt) REVERT: K 162 TYR cc_start: 0.7372 (t80) cc_final: 0.7153 (t80) REVERT: K 233 GLU cc_start: 0.8228 (tt0) cc_final: 0.8007 (tt0) REVERT: K 420 LEU cc_start: 0.9153 (mt) cc_final: 0.8889 (mp) REVERT: A 377 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8166 (ttm) REVERT: A 392 ASP cc_start: 0.8530 (t70) cc_final: 0.7993 (t0) REVERT: A 432 TYR cc_start: 0.9095 (OUTLIER) cc_final: 0.8068 (t80) REVERT: B 57 ASN cc_start: 0.8225 (t0) cc_final: 0.7705 (t0) REVERT: B 95 SER cc_start: 0.8733 (m) cc_final: 0.8481 (p) REVERT: B 291 GLN cc_start: 0.8572 (tp40) cc_final: 0.8348 (tm130) REVERT: B 297 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8607 (mtpt) REVERT: B 306 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8510 (mtm110) outliers start: 33 outliers final: 22 residues processed: 195 average time/residue: 0.5668 time to fit residues: 119.0041 Evaluate side-chains 199 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 412 HIS Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 380 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 8 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 273 ASN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.112023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.087077 restraints weight = 14986.028| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.45 r_work: 0.3065 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9779 Z= 0.144 Angle : 0.610 9.951 13273 Z= 0.299 Chirality : 0.044 0.216 1482 Planarity : 0.004 0.055 1725 Dihedral : 6.792 134.058 1446 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.78 % Allowed : 22.44 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.25), residues: 1199 helix: 2.05 (0.24), residues: 498 sheet: 0.14 (0.36), residues: 219 loop : -0.82 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 221 TYR 0.022 0.001 TYR A 103 PHE 0.012 0.001 PHE A 149 TRP 0.012 0.001 TRP A 21 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9779) covalent geometry : angle 0.61036 (13273) hydrogen bonds : bond 0.03767 ( 455) hydrogen bonds : angle 4.06511 ( 1341) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: K 39 GLU cc_start: 0.8164 (mp0) cc_final: 0.7756 (pt0) REVERT: K 103 ARG cc_start: 0.8531 (mmm-85) cc_final: 0.8295 (mmm-85) REVERT: K 113 MET cc_start: 0.7740 (tmm) cc_final: 0.7446 (tmt) REVERT: K 146 PHE cc_start: 0.8170 (m-80) cc_final: 0.7745 (m-10) REVERT: K 160 GLN cc_start: 0.7736 (pm20) cc_final: 0.7489 (pm20) REVERT: K 420 LEU cc_start: 0.9109 (mt) cc_final: 0.8835 (mp) REVERT: A 198 SER cc_start: 0.8907 (m) cc_final: 0.8632 (p) REVERT: A 377 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8138 (ttm) REVERT: A 392 ASP cc_start: 0.8534 (t70) cc_final: 0.8143 (t0) REVERT: A 432 TYR cc_start: 0.9017 (OUTLIER) cc_final: 0.8145 (t80) REVERT: B 57 ASN cc_start: 0.8141 (t0) cc_final: 0.7640 (t0) REVERT: B 297 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8618 (mtpt) REVERT: B 306 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8443 (mtm110) outliers start: 29 outliers final: 18 residues processed: 196 average time/residue: 0.5511 time to fit residues: 116.1624 Evaluate side-chains 195 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain K residue 162 TYR Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 412 HIS Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 380 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 113 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 107 ASN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS B 291 GLN B 416 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.111426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.086845 restraints weight = 14968.618| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.41 r_work: 0.3057 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9779 Z= 0.161 Angle : 0.622 12.217 13273 Z= 0.305 Chirality : 0.044 0.211 1482 Planarity : 0.004 0.057 1725 Dihedral : 6.753 133.534 1446 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.11 % Allowed : 23.30 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.25), residues: 1199 helix: 2.01 (0.24), residues: 498 sheet: 0.16 (0.36), residues: 219 loop : -0.79 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 221 TYR 0.025 0.001 TYR A 103 PHE 0.012 0.001 PHE A 149 TRP 0.011 0.001 TRP A 21 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 9779) covalent geometry : angle 0.62169 (13273) hydrogen bonds : bond 0.03907 ( 455) hydrogen bonds : angle 4.10805 ( 1341) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: K 39 GLU cc_start: 0.8163 (mp0) cc_final: 0.7743 (pt0) REVERT: K 103 ARG cc_start: 0.8531 (mmm-85) cc_final: 0.8254 (mmm-85) REVERT: K 113 MET cc_start: 0.7777 (tmm) cc_final: 0.7484 (tmt) REVERT: K 146 PHE cc_start: 0.8176 (m-80) cc_final: 0.7777 (m-10) REVERT: K 160 GLN cc_start: 0.7704 (pm20) cc_final: 0.7465 (pm20) REVERT: K 356 ILE cc_start: 0.8907 (mt) cc_final: 0.8691 (mp) REVERT: K 420 LEU cc_start: 0.9109 (mt) cc_final: 0.8839 (mp) REVERT: A 198 SER cc_start: 0.8903 (m) cc_final: 0.8649 (p) REVERT: A 377 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8128 (ttm) REVERT: A 392 ASP cc_start: 0.8572 (t70) cc_final: 0.8233 (t0) REVERT: A 432 TYR cc_start: 0.9045 (OUTLIER) cc_final: 0.8133 (t80) REVERT: B 57 ASN cc_start: 0.8172 (t0) cc_final: 0.7673 (t0) REVERT: B 297 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8589 (mtpt) REVERT: B 306 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8447 (mtm110) outliers start: 22 outliers final: 16 residues processed: 189 average time/residue: 0.5723 time to fit residues: 116.3029 Evaluate side-chains 195 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 412 HIS Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 380 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 96 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 2 optimal weight: 30.0000 chunk 30 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 107 ASN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.111349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.086674 restraints weight = 14939.534| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.41 r_work: 0.3055 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9779 Z= 0.164 Angle : 0.628 11.008 13273 Z= 0.307 Chirality : 0.044 0.203 1482 Planarity : 0.004 0.057 1725 Dihedral : 6.726 133.479 1446 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.49 % Allowed : 23.20 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.25), residues: 1199 helix: 1.92 (0.24), residues: 504 sheet: 0.17 (0.36), residues: 219 loop : -0.82 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 221 TYR 0.025 0.002 TYR A 103 PHE 0.012 0.001 PHE A 149 TRP 0.011 0.001 TRP A 21 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 9779) covalent geometry : angle 0.62756 (13273) hydrogen bonds : bond 0.03923 ( 455) hydrogen bonds : angle 4.09574 ( 1341) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3827.69 seconds wall clock time: 66 minutes 2.93 seconds (3962.93 seconds total)