Starting phenix.real_space_refine on Mon Mar 11 02:58:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8p_24241/03_2024/7n8p_24241.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8p_24241/03_2024/7n8p_24241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8p_24241/03_2024/7n8p_24241.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8p_24241/03_2024/7n8p_24241.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8p_24241/03_2024/7n8p_24241.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8p_24241/03_2024/7n8p_24241.pdb" } resolution = 3.42 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= 0.006 sd= 0.043 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: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4438 2.51 5 N 1140 2.21 5 O 1140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 15": "NH1" <-> "NH2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B GLU 203": "OE1" <-> "OE2" Residue "B GLU 235": "OE1" <-> "OE2" Residue "B GLU 414": "OE1" <-> "OE2" Residue "B GLU 459": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6758 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3379 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 19, 'TRANS': 430} Chain: "B" Number of atoms: 3379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3379 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 19, 'TRANS': 430} Time building chain proxies: 4.50, per 1000 atoms: 0.67 Number of scatterers: 6758 At special positions: 0 Unit cell: (76.504, 76.504, 114.232, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1140 8.00 N 1140 7.00 C 4438 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 - 3.50 Amino acid : False - 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: 2.41 Conformation dependent library (CDL) restraints added in 1.3 seconds 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 74.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 14 through 27 removed outlier: 3.996A pdb=" N GLN A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 69 removed outlier: 3.530A pdb=" N ALA A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA A 67 " --> pdb=" O GLN A 63 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL A 69 " --> pdb=" O MET A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 100 removed outlier: 3.717A pdb=" N LEU A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU A 89 " --> pdb=" O CYS A 85 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 98 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.760A pdb=" N GLY A 105 " --> pdb=" O PRO A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 116 removed outlier: 4.172A pdb=" N GLY A 114 " --> pdb=" O PRO A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 132 removed outlier: 3.651A pdb=" N LEU A 128 " --> pdb=" O TRP A 124 " (cutoff:3.500A) Proline residue: A 129 - end of helix removed outlier: 3.528A pdb=" N PHE A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 141 Processing helix chain 'A' and resid 148 through 165 removed outlier: 4.047A pdb=" N ILE A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 190 removed outlier: 3.678A pdb=" N ARG A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 201 removed outlier: 3.645A pdb=" N ILE A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 224 removed outlier: 3.728A pdb=" N ILE A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 removed outlier: 4.153A pdb=" N PHE A 232 " --> pdb=" O MET A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 removed outlier: 3.526A pdb=" N LEU A 252 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 281 removed outlier: 3.531A pdb=" N ILE A 257 " --> pdb=" O TRP A 253 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY A 259 " --> pdb=" O TYR A 255 " (cutoff:3.500A) Proline residue: A 267 - end of helix removed outlier: 3.978A pdb=" N ASP A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 304 removed outlier: 4.051A pdb=" N LEU A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N CYS A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 349 removed outlier: 3.719A pdb=" N PHE A 335 " --> pdb=" O GLY A 331 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE A 342 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 379 removed outlier: 3.778A pdb=" N VAL A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU A 377 " --> pdb=" O MET A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 395 removed outlier: 4.056A pdb=" N PHE A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 404 through 417 removed outlier: 3.627A pdb=" N GLY A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 440 removed outlier: 3.535A pdb=" N THR A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 435 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 448 through 460 removed outlier: 4.028A pdb=" N ALA A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 26 removed outlier: 4.035A pdb=" N ARG B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU B 26 " --> pdb=" O ILE B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 69 removed outlier: 3.947A pdb=" N MET B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRP B 59 " --> pdb=" O LYS B 55 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL B 69 " --> pdb=" O MET B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 101 removed outlier: 4.032A pdb=" N SER B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU B 89 " --> pdb=" O CYS B 85 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 116 removed outlier: 3.629A pdb=" N GLY B 114 " --> pdb=" O PRO B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 132 Proline residue: B 129 - end of helix Processing helix chain 'B' and resid 134 through 141 removed outlier: 3.653A pdb=" N GLY B 141 " --> pdb=" O GLY B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 165 removed outlier: 4.166A pdb=" N ILE B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.920A pdb=" N HIS B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 185 through 190 removed outlier: 3.668A pdb=" N PHE B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 201 removed outlier: 3.603A pdb=" N GLY B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B 197 " --> pdb=" O PRO B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 233 removed outlier: 3.752A pdb=" N MET B 228 " --> pdb=" O MET B 224 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE B 232 " --> pdb=" O MET B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 252 removed outlier: 3.748A pdb=" N LEU B 252 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 281 removed outlier: 3.601A pdb=" N ILE B 257 " --> pdb=" O TRP B 253 " (cutoff:3.500A) Proline residue: B 267 - end of helix removed outlier: 4.137A pdb=" N ASP B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 308 removed outlier: 3.943A pdb=" N LEU B 293 " --> pdb=" O THR B 289 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY B 306 " --> pdb=" O CYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 348 removed outlier: 4.099A pdb=" N PHE B 335 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 379 removed outlier: 3.885A pdb=" N LEU B 363 " --> pdb=" O PRO B 359 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL B 374 " --> pdb=" O ALA B 370 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU B 377 " --> pdb=" O MET B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 395 removed outlier: 4.543A pdb=" N GLY B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 417 removed outlier: 3.554A pdb=" N ILE B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 438 removed outlier: 3.675A pdb=" N THR B 433 " --> pdb=" O GLY B 429 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 435 " --> pdb=" O GLY B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 448 through 460 removed outlier: 3.599A pdb=" N GLN B 456 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B 457 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN B 460 " --> pdb=" O GLN B 456 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1128 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: 1.82 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2133 1.34 - 1.46: 1264 1.46 - 1.57: 3431 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 6902 Sorted by residual: bond pdb=" C ILE A 109 " pdb=" N PRO A 110 " ideal model delta sigma weight residual 1.334 1.382 -0.049 8.40e-03 1.42e+04 3.34e+01 bond pdb=" C ALA A 358 " pdb=" N PRO A 359 " ideal model delta sigma weight residual 1.334 1.378 -0.044 8.40e-03 1.42e+04 2.75e+01 bond pdb=" C LEU B 128 " pdb=" N PRO B 129 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.62e+00 bond pdb=" CA ILE B 109 " pdb=" C ILE B 109 " ideal model delta sigma weight residual 1.520 1.535 -0.015 8.80e-03 1.29e+04 2.85e+00 bond pdb=" CG1 ILE A 197 " pdb=" CD1 ILE A 197 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.15e+00 ... (remaining 6897 not shown) Histogram of bond angle deviations from ideal: 99.54 - 106.44: 209 106.44 - 113.33: 3695 113.33 - 120.22: 2791 120.22 - 127.12: 2599 127.12 - 134.01: 72 Bond angle restraints: 9366 Sorted by residual: angle pdb=" N LEU A 163 " pdb=" CA LEU A 163 " pdb=" C LEU A 163 " ideal model delta sigma weight residual 114.75 104.28 10.47 1.26e+00 6.30e-01 6.90e+01 angle pdb=" C GLY B 108 " pdb=" N ILE B 109 " pdb=" CA ILE B 109 " ideal model delta sigma weight residual 120.24 124.27 -4.03 6.30e-01 2.52e+00 4.09e+01 angle pdb=" C GLY A 108 " pdb=" N ILE A 109 " pdb=" CA ILE A 109 " ideal model delta sigma weight residual 120.24 122.94 -2.70 6.30e-01 2.52e+00 1.83e+01 angle pdb=" CA LEU A 163 " pdb=" C LEU A 163 " pdb=" N ASP A 164 " ideal model delta sigma weight residual 119.80 114.74 5.06 1.34e+00 5.57e-01 1.42e+01 angle pdb=" C ASN A 318 " pdb=" N LEU A 319 " pdb=" CA LEU A 319 " ideal model delta sigma weight residual 121.54 127.98 -6.44 1.91e+00 2.74e-01 1.14e+01 ... (remaining 9361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 3525 16.85 - 33.70: 391 33.70 - 50.55: 85 50.55 - 67.40: 7 67.40 - 84.25: 4 Dihedral angle restraints: 4012 sinusoidal: 1524 harmonic: 2488 Sorted by residual: dihedral pdb=" CA LEU A 301 " pdb=" C LEU A 301 " pdb=" N CYS A 302 " pdb=" CA CYS A 302 " ideal model delta harmonic sigma weight residual 180.00 151.80 28.20 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA VAL B 162 " pdb=" C VAL B 162 " pdb=" N LEU B 163 " pdb=" CA LEU B 163 " ideal model delta harmonic sigma weight residual 180.00 152.53 27.47 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA PHE A 317 " pdb=" C PHE A 317 " pdb=" N ASN A 318 " pdb=" CA ASN A 318 " ideal model delta harmonic sigma weight residual 180.00 156.45 23.55 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 4009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 922 0.065 - 0.131: 162 0.131 - 0.196: 15 0.196 - 0.261: 1 0.261 - 0.327: 2 Chirality restraints: 1102 Sorted by residual: chirality pdb=" CB ILE A 356 " pdb=" CA ILE A 356 " pdb=" CG1 ILE A 356 " pdb=" CG2 ILE A 356 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CB VAL A 162 " pdb=" CA VAL A 162 " pdb=" CG1 VAL A 162 " pdb=" CG2 VAL A 162 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB VAL A 41 " pdb=" CA VAL A 41 " pdb=" CG1 VAL A 41 " pdb=" CG2 VAL A 41 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.80e-01 ... (remaining 1099 not shown) Planarity restraints: 1176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 75 " -0.049 5.00e-02 4.00e+02 7.33e-02 8.59e+00 pdb=" N PRO A 76 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 423 " 0.042 5.00e-02 4.00e+02 6.21e-02 6.18e+00 pdb=" N PRO B 424 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 424 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 424 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 266 " -0.038 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO B 267 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 267 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 267 " -0.032 5.00e-02 4.00e+02 ... (remaining 1173 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1834 2.80 - 3.33: 6031 3.33 - 3.85: 11095 3.85 - 4.38: 13324 4.38 - 4.90: 22660 Nonbonded interactions: 54944 Sorted by model distance: nonbonded pdb=" O LEU B 345 " pdb=" OG SER B 349 " model vdw 2.276 2.440 nonbonded pdb=" OH TYR B 94 " pdb=" OG SER B 350 " model vdw 2.291 2.440 nonbonded pdb=" OG SER A 86 " pdb=" O GLY A 141 " model vdw 2.306 2.440 nonbonded pdb=" O VAL B 412 " pdb=" OG1 THR B 416 " model vdw 2.308 2.440 nonbonded pdb=" O LEU B 435 " pdb=" OG1 THR B 439 " model vdw 2.311 2.440 ... (remaining 54939 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.310 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: 1.930 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.070 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 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 0.071 6902 Z= 0.341 Angle : 0.891 11.422 9366 Z= 0.504 Chirality : 0.051 0.327 1102 Planarity : 0.008 0.073 1176 Dihedral : 14.416 84.252 2440 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.29 % Allowed : 9.44 % Favored : 90.27 % 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: -5.50 (0.20), residues: 896 helix: -3.60 (0.13), residues: 668 sheet: None (None), residues: 0 loop : -2.91 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 124 HIS 0.003 0.001 HIS B 284 PHE 0.025 0.002 PHE B 219 TYR 0.018 0.002 TYR B 419 ARG 0.002 0.000 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.746 Fit side-chains REVERT: A 167 ARG cc_start: 0.7064 (mtt90) cc_final: 0.6831 (mtm180) REVERT: B 38 MET cc_start: 0.7506 (mmt) cc_final: 0.7300 (mmt) outliers start: 2 outliers final: 1 residues processed: 106 average time/residue: 0.1704 time to fit residues: 25.1339 Evaluate side-chains 79 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.0670 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 0.0170 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 284 HIS A 418 ASN A 460 GLN B 61 GLN ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 HIS B 284 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6902 Z= 0.208 Angle : 0.562 8.867 9366 Z= 0.286 Chirality : 0.040 0.139 1102 Planarity : 0.005 0.044 1176 Dihedral : 5.356 35.204 962 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.18 % Allowed : 14.90 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.46 (0.26), residues: 896 helix: -2.18 (0.18), residues: 676 sheet: None (None), residues: 0 loop : -1.92 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 124 HIS 0.002 0.000 HIS B 284 PHE 0.011 0.001 PHE B 307 TYR 0.006 0.001 TYR A 94 ARG 0.003 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.734 Fit side-chains REVERT: A 167 ARG cc_start: 0.7026 (mtt90) cc_final: 0.6826 (mtm180) REVERT: B 38 MET cc_start: 0.7665 (mmt) cc_final: 0.7391 (mmt) outliers start: 8 outliers final: 3 residues processed: 88 average time/residue: 0.1357 time to fit residues: 17.7521 Evaluate side-chains 77 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain B residue 264 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6902 Z= 0.287 Angle : 0.580 8.475 9366 Z= 0.292 Chirality : 0.042 0.143 1102 Planarity : 0.005 0.045 1176 Dihedral : 5.223 33.809 962 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.47 % Allowed : 16.67 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.68 (0.27), residues: 896 helix: -1.59 (0.19), residues: 674 sheet: None (None), residues: 0 loop : -1.76 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 124 HIS 0.002 0.000 HIS A 70 PHE 0.013 0.001 PHE B 307 TYR 0.013 0.001 TYR B 419 ARG 0.002 0.000 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.774 Fit side-chains REVERT: B 38 MET cc_start: 0.7762 (mmt) cc_final: 0.7411 (mmt) outliers start: 10 outliers final: 9 residues processed: 80 average time/residue: 0.1494 time to fit residues: 17.8531 Evaluate side-chains 81 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 318 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 54 optimal weight: 0.4980 chunk 82 optimal weight: 0.2980 chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6902 Z= 0.172 Angle : 0.518 7.182 9366 Z= 0.262 Chirality : 0.039 0.135 1102 Planarity : 0.004 0.043 1176 Dihedral : 4.756 35.320 960 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.92 % Allowed : 18.73 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.08 (0.29), residues: 896 helix: -1.13 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -1.60 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 59 HIS 0.001 0.000 HIS A 281 PHE 0.011 0.001 PHE B 307 TYR 0.015 0.001 TYR B 419 ARG 0.002 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.765 Fit side-chains REVERT: B 38 MET cc_start: 0.7744 (mmt) cc_final: 0.7419 (mmt) outliers start: 13 outliers final: 6 residues processed: 92 average time/residue: 0.1468 time to fit residues: 19.9745 Evaluate side-chains 82 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 341 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 29 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6902 Z= 0.207 Angle : 0.531 7.403 9366 Z= 0.266 Chirality : 0.040 0.134 1102 Planarity : 0.004 0.045 1176 Dihedral : 4.677 33.757 960 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.65 % Allowed : 19.47 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.76 (0.29), residues: 896 helix: -0.90 (0.21), residues: 674 sheet: None (None), residues: 0 loop : -1.48 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 124 HIS 0.001 0.000 HIS B 284 PHE 0.014 0.001 PHE A 166 TYR 0.016 0.001 TYR B 419 ARG 0.002 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 0.793 Fit side-chains REVERT: A 38 MET cc_start: 0.7070 (mmt) cc_final: 0.6694 (mmp) REVERT: B 38 MET cc_start: 0.7768 (mmt) cc_final: 0.7456 (mmt) outliers start: 18 outliers final: 12 residues processed: 93 average time/residue: 0.1333 time to fit residues: 19.1375 Evaluate side-chains 90 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 388 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 72 optimal weight: 0.0570 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 83 optimal weight: 0.0470 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6902 Z= 0.150 Angle : 0.502 7.753 9366 Z= 0.252 Chirality : 0.039 0.132 1102 Planarity : 0.004 0.043 1176 Dihedral : 4.488 35.310 960 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.65 % Allowed : 20.94 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.28 (0.29), residues: 896 helix: -0.55 (0.21), residues: 672 sheet: None (None), residues: 0 loop : -1.32 (0.45), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 253 HIS 0.001 0.000 HIS A 284 PHE 0.018 0.001 PHE B 307 TYR 0.014 0.001 TYR B 419 ARG 0.002 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 0.699 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.7073 (mmt) cc_final: 0.6713 (mmp) REVERT: A 461 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6370 (pp) REVERT: B 38 MET cc_start: 0.7743 (mmt) cc_final: 0.7450 (mmt) outliers start: 18 outliers final: 11 residues processed: 105 average time/residue: 0.1556 time to fit residues: 23.4950 Evaluate side-chains 90 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 86 optimal weight: 0.0970 chunk 54 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6902 Z= 0.171 Angle : 0.527 9.501 9366 Z= 0.261 Chirality : 0.040 0.131 1102 Planarity : 0.004 0.044 1176 Dihedral : 4.445 34.036 960 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.80 % Allowed : 21.83 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.07 (0.30), residues: 896 helix: -0.40 (0.21), residues: 672 sheet: None (None), residues: 0 loop : -1.23 (0.45), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 124 HIS 0.001 0.000 HIS A 284 PHE 0.018 0.001 PHE A 379 TYR 0.012 0.001 TYR B 419 ARG 0.006 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 0.731 Fit side-chains REVERT: A 38 MET cc_start: 0.7044 (mmt) cc_final: 0.6739 (mmp) REVERT: A 461 LEU cc_start: 0.6571 (OUTLIER) cc_final: 0.6354 (pp) REVERT: B 38 MET cc_start: 0.7744 (mmt) cc_final: 0.7427 (mmt) outliers start: 19 outliers final: 16 residues processed: 94 average time/residue: 0.1334 time to fit residues: 19.1776 Evaluate side-chains 93 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 76 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 421 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 68 optimal weight: 0.2980 chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 75 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6902 Z= 0.156 Angle : 0.522 9.459 9366 Z= 0.258 Chirality : 0.039 0.131 1102 Planarity : 0.004 0.045 1176 Dihedral : 4.362 34.570 960 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.65 % Allowed : 21.98 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.79 (0.30), residues: 896 helix: -0.19 (0.21), residues: 672 sheet: None (None), residues: 0 loop : -1.15 (0.45), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 253 HIS 0.001 0.000 HIS A 284 PHE 0.016 0.001 PHE B 307 TYR 0.012 0.001 TYR A 419 ARG 0.005 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 461 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.6117 (pp) REVERT: B 38 MET cc_start: 0.7748 (mmt) cc_final: 0.7480 (mmt) outliers start: 18 outliers final: 15 residues processed: 99 average time/residue: 0.1251 time to fit residues: 19.0050 Evaluate side-chains 94 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 421 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6902 Z= 0.189 Angle : 0.546 9.612 9366 Z= 0.267 Chirality : 0.040 0.138 1102 Planarity : 0.004 0.046 1176 Dihedral : 4.367 33.139 960 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.80 % Allowed : 22.12 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.67 (0.30), residues: 896 helix: -0.10 (0.21), residues: 672 sheet: None (None), residues: 0 loop : -1.10 (0.45), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 253 HIS 0.001 0.000 HIS A 284 PHE 0.017 0.001 PHE B 307 TYR 0.010 0.001 TYR A 419 ARG 0.005 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 0.772 Fit side-chains REVERT: A 461 LEU cc_start: 0.6297 (OUTLIER) cc_final: 0.6079 (pp) REVERT: B 38 MET cc_start: 0.7796 (mmt) cc_final: 0.7440 (mmt) outliers start: 19 outliers final: 18 residues processed: 94 average time/residue: 0.1321 time to fit residues: 19.0143 Evaluate side-chains 97 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 421 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6902 Z= 0.203 Angle : 0.554 9.594 9366 Z= 0.272 Chirality : 0.041 0.138 1102 Planarity : 0.004 0.047 1176 Dihedral : 4.397 32.486 960 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.80 % Allowed : 22.42 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.63 (0.30), residues: 896 helix: -0.07 (0.21), residues: 672 sheet: None (None), residues: 0 loop : -1.12 (0.45), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 124 HIS 0.001 0.000 HIS A 284 PHE 0.019 0.001 PHE B 307 TYR 0.010 0.001 TYR A 419 ARG 0.005 0.000 ARG B 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 0.713 Fit side-chains REVERT: A 461 LEU cc_start: 0.6274 (OUTLIER) cc_final: 0.6048 (pp) REVERT: B 38 MET cc_start: 0.7801 (mmt) cc_final: 0.7467 (mmt) outliers start: 19 outliers final: 16 residues processed: 94 average time/residue: 0.1267 time to fit residues: 18.2478 Evaluate side-chains 94 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 388 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 9 optimal weight: 0.0470 chunk 13 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.139745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.124171 restraints weight = 9395.889| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.58 r_work: 0.3437 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6902 Z= 0.175 Angle : 0.550 11.027 9366 Z= 0.268 Chirality : 0.040 0.142 1102 Planarity : 0.004 0.046 1176 Dihedral : 4.361 32.864 960 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.95 % Allowed : 22.42 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.47 (0.30), residues: 896 helix: 0.05 (0.21), residues: 672 sheet: None (None), residues: 0 loop : -1.06 (0.45), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 253 HIS 0.001 0.000 HIS A 284 PHE 0.018 0.001 PHE B 307 TYR 0.010 0.001 TYR A 419 ARG 0.005 0.000 ARG B 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1483.61 seconds wall clock time: 27 minutes 50.96 seconds (1670.96 seconds total)