Starting phenix.real_space_refine on Wed Aug 5 14:44:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nyg_49934/08_2026/9nyg_49934.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nyg_49934/08_2026/9nyg_49934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nyg_49934/08_2026/9nyg_49934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nyg_49934/08_2026/9nyg_49934.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nyg_49934/08_2026/9nyg_49934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nyg_49934/08_2026/9nyg_49934.map" } resolution = 2.93 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= -0.000 sd= 0.011 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: 5 Type Number sf(0) Gaussians P 31 5.49 5 S 27 5.16 5 C 6285 2.51 5 N 1758 2.21 5 O 1960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10061 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1239 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain breaks: 1 Chain: "A" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2256 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 5, 'TRANS': 268} Chain breaks: 3 Chain: "G" Number of atoms: 1329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1329 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 2, 'TRANS': 165} Chain breaks: 3 Chain: "B" Number of atoms: 4601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4601 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 22, 'TRANS': 548} Chain breaks: 5 Chain: "E" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 313 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "F" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 323 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Time building chain proxies: 1.64, per 1000 atoms: 0.16 Number of scatterers: 10061 At special positions: 0 Unit cell: (81.2, 103.675, 165.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 31 15.00 O 1960 8.00 N 1758 7.00 C 6285 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: 0.69 Conformation dependent library (CDL) restraints added in 315.5 milliseconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2244 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 2 sheets defined 51.1% alpha, 3.5% beta 10 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'C' and resid 34 through 44 removed outlier: 3.910A pdb=" N LEU C 38 " --> pdb=" O TRP C 34 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA C 39 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 71 removed outlier: 4.216A pdb=" N SER C 71 " --> pdb=" O ASN C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 83 Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 95 through 100 removed outlier: 3.867A pdb=" N PHE C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 162 Processing helix chain 'C' and resid 166 through 174 removed outlier: 3.619A pdb=" N LEU C 174 " --> pdb=" O LEU C 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 28 removed outlier: 4.134A pdb=" N ARG A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 179 removed outlier: 3.936A pdb=" N TYR A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 209 removed outlier: 3.655A pdb=" N ILE A 192 " --> pdb=" O HIS A 188 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TRP A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A 200 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 238 Processing helix chain 'A' and resid 264 through 269 removed outlier: 4.205A pdb=" N ILE A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 296 removed outlier: 3.657A pdb=" N LEU A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 302 Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.675A pdb=" N ARG A 308 " --> pdb=" O ARG A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 313 Processing helix chain 'A' and resid 319 through 325 removed outlier: 3.827A pdb=" N LEU A 323 " --> pdb=" O GLN A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 334 through 342 removed outlier: 3.769A pdb=" N TYR A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.787A pdb=" N ALA A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 234 Processing helix chain 'G' and resid 239 through 245 Processing helix chain 'G' and resid 278 through 314 Processing helix chain 'G' and resid 315 through 317 No H-bonds generated for 'chain 'G' and resid 315 through 317' Processing helix chain 'G' and resid 356 through 360 removed outlier: 3.770A pdb=" N LEU G 360 " --> pdb=" O GLU G 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 356 through 360' Processing helix chain 'G' and resid 361 through 374 removed outlier: 3.504A pdb=" N ARG G 367 " --> pdb=" O GLU G 363 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER G 370 " --> pdb=" O ALA G 366 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASN G 371 " --> pdb=" O ARG G 367 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LEU G 372 " --> pdb=" O ALA G 368 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU G 373 " --> pdb=" O PHE G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 416 Processing helix chain 'G' and resid 426 through 440 Processing helix chain 'B' and resid 39 through 41 No H-bonds generated for 'chain 'B' and resid 39 through 41' Processing helix chain 'B' and resid 42 through 52 removed outlier: 3.586A pdb=" N GLY B 52 " --> pdb=" O ASP B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 152 through 156 removed outlier: 4.159A pdb=" N ALA B 156 " --> pdb=" O ASP B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 removed outlier: 3.555A pdb=" N ILE B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA B 166 " --> pdb=" O GLN B 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 161 through 166' Processing helix chain 'B' and resid 181 through 186 Processing helix chain 'B' and resid 187 through 192 Processing helix chain 'B' and resid 196 through 201 removed outlier: 3.700A pdb=" N GLU B 201 " --> pdb=" O ASN B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 217 removed outlier: 4.286A pdb=" N LYS B 207 " --> pdb=" O GLN B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 237 through 244 removed outlier: 3.624A pdb=" N ALA B 241 " --> pdb=" O TYR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.641A pdb=" N GLN B 255 " --> pdb=" O ASP B 252 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU B 256 " --> pdb=" O ILE B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 256' Processing helix chain 'B' and resid 257 through 267 removed outlier: 3.690A pdb=" N ASN B 267 " --> pdb=" O ASN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 305 removed outlier: 6.116A pdb=" N ASN B 302 " --> pdb=" O ASP B 298 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS B 305 " --> pdb=" O ASN B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 333 removed outlier: 3.730A pdb=" N LEU B 319 " --> pdb=" O SER B 315 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA B 320 " --> pdb=" O MET B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 370 Processing helix chain 'B' and resid 379 through 408 removed outlier: 4.404A pdb=" N GLN B 383 " --> pdb=" O PRO B 379 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLY B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU B 396 " --> pdb=" O TYR B 392 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG B 399 " --> pdb=" O GLY B 395 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU B 400 " --> pdb=" O GLU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 432 Processing helix chain 'B' and resid 433 through 442 Processing helix chain 'B' and resid 451 through 456 removed outlier: 3.529A pdb=" N TYR B 455 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS B 456 " --> pdb=" O SER B 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 451 through 456' Processing helix chain 'B' and resid 461 through 469 removed outlier: 4.067A pdb=" N ILE B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 488 Processing helix chain 'B' and resid 489 through 492 removed outlier: 3.602A pdb=" N TRP B 492 " --> pdb=" O ALA B 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 489 through 492' Processing helix chain 'B' and resid 532 through 552 Processing helix chain 'B' and resid 566 through 569 removed outlier: 4.240A pdb=" N VAL B 569 " --> pdb=" O PRO B 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 566 through 569' Processing helix chain 'B' and resid 595 through 610 removed outlier: 3.828A pdb=" N ILE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLU B 610 " --> pdb=" O ASN B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.534A pdb=" N LEU B 628 " --> pdb=" O PRO B 625 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL B 629 " --> pdb=" O SER B 626 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 625 through 629' Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 23 removed outlier: 5.589A pdb=" N ILE B 5 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LYS B 75 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS B 7 " --> pdb=" O GLN B 73 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP B 69 " --> pdb=" O TRP B 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 159 through 160 removed outlier: 6.104A pdb=" N ASN B 30 " --> pdb=" O VAL B 620 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ASP B 622 " --> pdb=" O ASN B 30 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE B 32 " --> pdb=" O ASP B 622 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL B 29 " --> pdb=" O HIS B 636 " (cutoff:3.500A) 349 hydrogen bonds defined for protein. 1032 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 1.43 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 1613 1.25 - 1.39: 2441 1.39 - 1.53: 5743 1.53 - 1.68: 457 1.68 - 1.82: 43 Bond restraints: 10297 Sorted by residual: bond pdb=" CG PRO B 558 " pdb=" CD PRO B 558 " ideal model delta sigma weight residual 1.503 1.110 0.393 3.40e-02 8.65e+02 1.33e+02 bond pdb=" CG PRO B 19 " pdb=" CD PRO B 19 " ideal model delta sigma weight residual 1.503 1.140 0.363 3.40e-02 8.65e+02 1.14e+02 bond pdb=" CB PRO B 558 " pdb=" CG PRO B 558 " ideal model delta sigma weight residual 1.492 1.193 0.299 5.00e-02 4.00e+02 3.58e+01 bond pdb=" C ILE C 93 " pdb=" N PRO C 94 " ideal model delta sigma weight residual 1.333 1.402 -0.069 1.44e-02 4.82e+03 2.29e+01 bond pdb=" C HIS C 49 " pdb=" N PRO C 50 " ideal model delta sigma weight residual 1.336 1.388 -0.052 1.20e-02 6.94e+03 1.87e+01 ... (remaining 10292 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.87: 13958 6.87 - 13.74: 53 13.74 - 20.62: 1 20.62 - 27.49: 1 27.49 - 34.36: 3 Bond angle restraints: 14016 Sorted by residual: angle pdb=" N PRO B 558 " pdb=" CD PRO B 558 " pdb=" CG PRO B 558 " ideal model delta sigma weight residual 103.20 73.13 30.07 1.50e+00 4.44e-01 4.02e+02 angle pdb=" CA PRO B 558 " pdb=" CB PRO B 558 " pdb=" CG PRO B 558 " ideal model delta sigma weight residual 104.50 70.14 34.36 1.90e+00 2.77e-01 3.27e+02 angle pdb=" N PRO B 19 " pdb=" CD PRO B 19 " pdb=" CG PRO B 19 " ideal model delta sigma weight residual 103.20 82.54 20.66 1.50e+00 4.44e-01 1.90e+02 angle pdb=" CB PRO B 558 " pdb=" CG PRO B 558 " pdb=" CD PRO B 558 " ideal model delta sigma weight residual 106.10 135.45 -29.35 3.20e+00 9.77e-02 8.41e+01 angle pdb=" CA PRO B 19 " pdb=" N PRO B 19 " pdb=" CD PRO B 19 " ideal model delta sigma weight residual 112.00 101.43 10.57 1.40e+00 5.10e-01 5.71e+01 ... (remaining 14011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.46: 5685 32.46 - 64.92: 508 64.92 - 97.39: 40 97.39 - 129.85: 0 129.85 - 162.31: 1 Dihedral angle restraints: 6234 sinusoidal: 2798 harmonic: 3436 Sorted by residual: dihedral pdb=" CA PHE C 59 " pdb=" C PHE C 59 " pdb=" N ILE C 60 " pdb=" CA ILE C 60 " ideal model delta harmonic sigma weight residual 180.00 152.96 27.04 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA GLU C 22 " pdb=" C GLU C 22 " pdb=" N ILE C 23 " pdb=" CA ILE C 23 " ideal model delta harmonic sigma weight residual 180.00 154.29 25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA ARG C 52 " pdb=" C ARG C 52 " pdb=" N LEU C 53 " pdb=" CA LEU C 53 " ideal model delta harmonic sigma weight residual -180.00 -155.75 -24.25 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 6231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1377 0.078 - 0.156: 183 0.156 - 0.234: 15 0.234 - 0.312: 5 0.312 - 0.390: 3 Chirality restraints: 1583 Sorted by residual: chirality pdb=" CB ILE C 93 " pdb=" CA ILE C 93 " pdb=" CG1 ILE C 93 " pdb=" CG2 ILE C 93 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CG LEU B 362 " pdb=" CB LEU B 362 " pdb=" CD1 LEU B 362 " pdb=" CD2 LEU B 362 " both_signs ideal model delta sigma weight residual False -2.59 -2.92 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CB ILE B 111 " pdb=" CA ILE B 111 " pdb=" CG1 ILE B 111 " pdb=" CG2 ILE B 111 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 1580 not shown) Planarity restraints: 1673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 18 " 0.082 5.00e-02 4.00e+02 1.15e-01 2.12e+01 pdb=" N PRO B 19 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO B 19 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 19 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 557 " -0.049 5.00e-02 4.00e+02 6.87e-02 7.56e+00 pdb=" N PRO B 558 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 558 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 558 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 470 " 0.044 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO B 471 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 471 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 471 " 0.037 5.00e-02 4.00e+02 ... (remaining 1670 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2492 2.80 - 3.32: 8712 3.32 - 3.85: 17684 3.85 - 4.37: 19772 4.37 - 4.90: 32417 Nonbonded interactions: 81077 Sorted by model distance: nonbonded pdb=" OG SER B 79 " pdb=" O ALA B 102 " model vdw 2.272 3.040 nonbonded pdb=" O THR B 515 " pdb=" OG1 THR B 515 " model vdw 2.292 3.040 nonbonded pdb=" O GLN B 91 " pdb=" OG1 THR B 94 " model vdw 2.320 3.040 nonbonded pdb=" O GLY A 226 " pdb=" OG SER A 230 " model vdw 2.324 3.040 nonbonded pdb=" O THR A 214 " pdb=" OG1 THR A 214 " model vdw 2.344 3.040 ... (remaining 81072 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: 7.310 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: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.270 Find NCS groups from input model: 0.040 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5765 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 : 0.008 0.393 10297 Z= 0.339 Angle : 1.146 34.359 14016 Z= 0.651 Chirality : 0.056 0.390 1583 Planarity : 0.007 0.115 1673 Dihedral : 21.924 162.309 3990 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.67 % Favored : 89.24 % Rotamer: Outliers : 2.76 % Allowed : 40.72 % Favored : 56.52 % 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: -3.66 (0.21), residues: 1134 helix: -2.08 (0.18), residues: 552 sheet: -1.94 (0.78), residues: 51 loop : -2.85 (0.23), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 358 TYR 0.021 0.002 TYR C 79 PHE 0.028 0.002 PHE B 172 TRP 0.018 0.002 TRP A 80 HIS 0.007 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00772 / 0.34 (10297) covalent geometry : angle 1.14558 / 0.65 (14016) hydrogen bonds : bond 0.15892 / 10.16 ( 373) hydrogen bonds : angle 7.06020 / 4.81 ( 1080) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.277 Fit side-chains REVERT: C 105 LYS cc_start: 0.2453 (OUTLIER) cc_final: 0.2119 (pttm) outliers start: 29 outliers final: 17 residues processed: 115 average time/residue: 0.3944 time to fit residues: 49.8036 Evaluate side-chains 100 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 180 HIS Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 648 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 ASN A 212 GLN G 410 GLN B 312 ASN B 623 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5002 r_free = 0.5002 target = 0.258732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.234641 restraints weight = 12934.980| |-----------------------------------------------------------------------------| r_work (start): 0.4825 rms_B_bonded: 1.57 r_work: 0.4727 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.4617 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.4617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6038 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10297 Z= 0.158 Angle : 0.651 6.931 14016 Z= 0.349 Chirality : 0.045 0.290 1583 Planarity : 0.005 0.047 1673 Dihedral : 17.543 155.663 1640 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.44 % Favored : 90.48 % Rotamer: Outliers : 8.56 % Allowed : 34.16 % Favored : 57.28 % 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: -2.92 (0.23), residues: 1134 helix: -1.19 (0.21), residues: 561 sheet: -2.33 (0.68), residues: 52 loop : -2.74 (0.24), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 457 TYR 0.014 0.001 TYR A 232 PHE 0.011 0.002 PHE B 172 TRP 0.011 0.001 TRP C 161 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (10297) covalent geometry : angle 0.65054 / 0.35 (14016) hydrogen bonds : bond 0.04594 / 3.08 ( 373) hydrogen bonds : angle 5.25231 / 3.61 ( 1080) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 92 time to evaluate : 0.251 Fit side-chains REVERT: C 105 LYS cc_start: 0.2731 (OUTLIER) cc_final: 0.0185 (tttp) REVERT: C 112 LEU cc_start: 0.5804 (OUTLIER) cc_final: 0.5438 (mp) REVERT: A 367 MET cc_start: 0.4852 (OUTLIER) cc_final: 0.2861 (mtt) REVERT: B 621 LEU cc_start: 0.6458 (OUTLIER) cc_final: 0.5990 (mt) outliers start: 90 outliers final: 40 residues processed: 173 average time/residue: 0.3772 time to fit residues: 72.3554 Evaluate side-chains 125 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 81 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 626 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 100 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 141 ASN A 322 HIS B 180 HIS ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4975 r_free = 0.4975 target = 0.254307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.229799 restraints weight = 12884.590| |-----------------------------------------------------------------------------| r_work (start): 0.4791 rms_B_bonded: 1.56 r_work: 0.4691 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.4582 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.4582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6133 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10297 Z= 0.166 Angle : 0.645 11.051 14016 Z= 0.345 Chirality : 0.045 0.259 1583 Planarity : 0.004 0.046 1673 Dihedral : 17.370 150.873 1613 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.58 % Favored : 89.33 % Rotamer: Outliers : 9.99 % Allowed : 33.21 % Favored : 56.80 % 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: -2.66 (0.23), residues: 1134 helix: -0.91 (0.21), residues: 559 sheet: -2.28 (0.68), residues: 52 loop : -2.69 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 66 TYR 0.017 0.001 TYR A 232 PHE 0.014 0.002 PHE B 157 TRP 0.012 0.002 TRP B 641 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (10297) covalent geometry : angle 0.64499 / 0.35 (14016) hydrogen bonds : bond 0.04426 / 2.93 ( 373) hydrogen bonds : angle 5.06974 / 3.47 ( 1080) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 80 time to evaluate : 0.382 Fit side-chains REVERT: C 43 LYS cc_start: 0.6913 (OUTLIER) cc_final: 0.6251 (tttm) REVERT: C 105 LYS cc_start: 0.2691 (OUTLIER) cc_final: -0.0227 (ttpp) REVERT: C 106 ASN cc_start: 0.5839 (OUTLIER) cc_final: 0.4788 (m110) REVERT: C 112 LEU cc_start: 0.5828 (OUTLIER) cc_final: 0.5453 (mp) REVERT: A 156 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6556 (tp) REVERT: A 193 MET cc_start: 0.6602 (OUTLIER) cc_final: 0.6227 (mpp) REVERT: A 224 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.5665 (tpm170) REVERT: A 359 PHE cc_start: 0.5852 (OUTLIER) cc_final: 0.5031 (m-80) REVERT: A 367 MET cc_start: 0.4979 (OUTLIER) cc_final: 0.2964 (mtt) REVERT: B 321 ASN cc_start: 0.5215 (OUTLIER) cc_final: 0.4432 (p0) REVERT: B 505 ILE cc_start: 0.3808 (OUTLIER) cc_final: 0.2042 (tt) REVERT: B 621 LEU cc_start: 0.6438 (OUTLIER) cc_final: 0.5975 (mt) outliers start: 105 outliers final: 47 residues processed: 176 average time/residue: 0.3986 time to fit residues: 77.5991 Evaluate side-chains 136 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 77 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 29 CYS Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain G residue 343 GLN Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 180 HIS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 648 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 15 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 89 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 8 optimal weight: 0.0270 chunk 20 optimal weight: 0.6980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 ASN ** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 ASN ** 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 = 0.4987 r_free = 0.4987 target = 0.255570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.231250 restraints weight = 12899.867| |-----------------------------------------------------------------------------| r_work (start): 0.4802 rms_B_bonded: 1.57 r_work: 0.4698 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4587 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.4587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10297 Z= 0.137 Angle : 0.621 9.214 14016 Z= 0.330 Chirality : 0.043 0.232 1583 Planarity : 0.004 0.053 1673 Dihedral : 17.289 145.766 1613 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.49 % Favored : 89.42 % Rotamer: Outliers : 9.32 % Allowed : 33.87 % Favored : 56.80 % 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: -2.43 (0.24), residues: 1134 helix: -0.67 (0.22), residues: 557 sheet: -2.26 (0.69), residues: 52 loop : -2.62 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 297 TYR 0.014 0.001 TYR A 232 PHE 0.017 0.001 PHE B 157 TRP 0.012 0.001 TRP B 641 HIS 0.012 0.001 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (10297) covalent geometry : angle 0.62109 / 0.33 (14016) hydrogen bonds : bond 0.03963 / 2.64 ( 373) hydrogen bonds : angle 4.88314 / 3.34 ( 1080) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 85 time to evaluate : 0.366 Fit side-chains REVERT: C 43 LYS cc_start: 0.6881 (OUTLIER) cc_final: 0.6265 (tttm) REVERT: C 105 LYS cc_start: 0.2838 (OUTLIER) cc_final: -0.0192 (tmtm) REVERT: C 106 ASN cc_start: 0.5672 (OUTLIER) cc_final: 0.4487 (m-40) REVERT: C 112 LEU cc_start: 0.5795 (OUTLIER) cc_final: 0.5472 (mp) REVERT: A 156 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6625 (tp) REVERT: A 193 MET cc_start: 0.6569 (OUTLIER) cc_final: 0.5188 (mpp) REVERT: A 224 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.5866 (tpm170) REVERT: A 359 PHE cc_start: 0.5780 (OUTLIER) cc_final: 0.4962 (m-80) REVERT: G 230 TRP cc_start: 0.3034 (p90) cc_final: 0.2782 (p90) REVERT: G 367 ARG cc_start: 0.4920 (ptt-90) cc_final: 0.4626 (ptt90) REVERT: B 442 MET cc_start: 0.4460 (tpt) cc_final: 0.4155 (mmm) REVERT: B 621 LEU cc_start: 0.6518 (OUTLIER) cc_final: 0.6038 (mt) outliers start: 98 outliers final: 48 residues processed: 176 average time/residue: 0.3890 time to fit residues: 75.4639 Evaluate side-chains 133 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 76 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 29 CYS Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 648 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 88 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 39 optimal weight: 0.0070 chunk 22 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 0.0670 chunk 53 optimal weight: 0.0470 chunk 52 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.3034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 141 ASN A 93 ASN ** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN B 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4997 r_free = 0.4997 target = 0.256859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.232902 restraints weight = 12919.259| |-----------------------------------------------------------------------------| r_work (start): 0.4813 rms_B_bonded: 1.57 r_work: 0.4712 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.4602 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.4602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6066 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10297 Z= 0.124 Angle : 0.606 9.632 14016 Z= 0.321 Chirality : 0.043 0.219 1583 Planarity : 0.004 0.064 1673 Dihedral : 17.214 140.788 1613 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.23 % Favored : 89.68 % Rotamer: Outliers : 7.99 % Allowed : 35.20 % Favored : 56.80 % 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: -2.21 (0.25), residues: 1134 helix: -0.45 (0.22), residues: 556 sheet: -2.30 (0.69), residues: 52 loop : -2.54 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 297 TYR 0.014 0.001 TYR A 232 PHE 0.020 0.001 PHE B 157 TRP 0.015 0.001 TRP C 161 HIS 0.005 0.001 HIS B 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (10297) covalent geometry : angle 0.60578 / 0.32 (14016) hydrogen bonds : bond 0.03791 / 2.56 ( 373) hydrogen bonds : angle 4.70917 / 3.23 ( 1080) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 84 time to evaluate : 0.363 Fit side-chains REVERT: C 43 LYS cc_start: 0.6866 (OUTLIER) cc_final: 0.6157 (tttm) REVERT: C 105 LYS cc_start: 0.2800 (OUTLIER) cc_final: 0.0109 (tttp) REVERT: C 112 LEU cc_start: 0.5805 (OUTLIER) cc_final: 0.5505 (mp) REVERT: A 37 PHE cc_start: 0.4901 (OUTLIER) cc_final: 0.4684 (m-10) REVERT: A 193 MET cc_start: 0.6626 (OUTLIER) cc_final: 0.6318 (mpp) REVERT: A 224 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.5871 (tpm170) REVERT: A 359 PHE cc_start: 0.5740 (OUTLIER) cc_final: 0.5019 (m-80) REVERT: G 230 TRP cc_start: 0.2956 (p90) cc_final: 0.2699 (p90) REVERT: B 321 ASN cc_start: 0.5217 (OUTLIER) cc_final: 0.4522 (p0) REVERT: B 442 MET cc_start: 0.4555 (tpt) cc_final: 0.4173 (mmm) REVERT: B 505 ILE cc_start: 0.3816 (OUTLIER) cc_final: 0.1986 (tt) REVERT: B 621 LEU cc_start: 0.6491 (OUTLIER) cc_final: 0.6039 (mt) outliers start: 84 outliers final: 40 residues processed: 160 average time/residue: 0.3810 time to fit residues: 67.6822 Evaluate side-chains 130 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 80 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 29 CYS Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 343 GLN Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 648 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 50 optimal weight: 0.0270 chunk 57 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 81 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 ASN A 212 GLN A 239 ASN ** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4980 r_free = 0.4980 target = 0.254750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.230428 restraints weight = 12939.489| |-----------------------------------------------------------------------------| r_work (start): 0.4796 rms_B_bonded: 1.56 r_work: 0.4693 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.4582 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.4582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6122 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10297 Z= 0.145 Angle : 0.631 11.824 14016 Z= 0.333 Chirality : 0.043 0.214 1583 Planarity : 0.004 0.040 1673 Dihedral : 17.206 137.772 1613 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.76 % Favored : 89.15 % Rotamer: Outliers : 7.90 % Allowed : 35.97 % Favored : 56.14 % 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: -2.17 (0.25), residues: 1134 helix: -0.45 (0.22), residues: 555 sheet: -2.22 (0.69), residues: 52 loop : -2.49 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 297 TYR 0.015 0.001 TYR A 232 PHE 0.024 0.001 PHE B 157 TRP 0.011 0.001 TRP B 641 HIS 0.005 0.001 HIS B 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (10297) covalent geometry : angle 0.63094 / 0.33 (14016) hydrogen bonds : bond 0.03899 / 2.63 ( 373) hydrogen bonds : angle 4.69899 / 3.21 ( 1080) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 80 time to evaluate : 0.297 Fit side-chains REVERT: C 43 LYS cc_start: 0.6870 (OUTLIER) cc_final: 0.6243 (tttm) REVERT: C 105 LYS cc_start: 0.2859 (OUTLIER) cc_final: -0.0037 (tttp) REVERT: C 106 ASN cc_start: 0.5703 (OUTLIER) cc_final: 0.4461 (m-40) REVERT: C 112 LEU cc_start: 0.5779 (OUTLIER) cc_final: 0.5470 (mp) REVERT: A 37 PHE cc_start: 0.5023 (OUTLIER) cc_final: 0.4764 (m-10) REVERT: A 193 MET cc_start: 0.6614 (OUTLIER) cc_final: 0.6273 (mpp) REVERT: A 224 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.5836 (tpm170) REVERT: A 359 PHE cc_start: 0.5794 (OUTLIER) cc_final: 0.4963 (m-80) REVERT: B 321 ASN cc_start: 0.5122 (OUTLIER) cc_final: 0.4562 (p0) REVERT: B 442 MET cc_start: 0.4480 (tpt) cc_final: 0.4211 (mmm) REVERT: B 505 ILE cc_start: 0.3852 (OUTLIER) cc_final: 0.2056 (tt) REVERT: B 621 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.6018 (mt) outliers start: 83 outliers final: 50 residues processed: 157 average time/residue: 0.3389 time to fit residues: 59.2016 Evaluate side-chains 138 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 77 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 29 CYS Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain G residue 343 GLN Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 648 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 82 optimal weight: 7.9990 chunk 21 optimal weight: 0.0270 chunk 32 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 68 optimal weight: 0.0000 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 ASN A 212 GLN ** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4989 r_free = 0.4989 target = 0.256004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.231907 restraints weight = 12844.425| |-----------------------------------------------------------------------------| r_work (start): 0.4812 rms_B_bonded: 1.56 r_work: 0.4710 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.4599 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.4599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6087 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10297 Z= 0.128 Angle : 0.617 12.880 14016 Z= 0.325 Chirality : 0.043 0.211 1583 Planarity : 0.004 0.041 1673 Dihedral : 17.166 135.750 1613 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.05 % Favored : 89.86 % Rotamer: Outliers : 7.23 % Allowed : 36.63 % Favored : 56.14 % 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: -2.06 (0.25), residues: 1134 helix: -0.35 (0.22), residues: 556 sheet: -2.24 (0.70), residues: 52 loop : -2.44 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 211 TYR 0.015 0.001 TYR A 232 PHE 0.027 0.001 PHE B 157 TRP 0.011 0.001 TRP B 641 HIS 0.004 0.001 HIS B 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (10297) covalent geometry : angle 0.61700 / 0.32 (14016) hydrogen bonds : bond 0.03718 / 2.53 ( 373) hydrogen bonds : angle 4.59397 / 3.15 ( 1080) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 84 time to evaluate : 0.303 Fit side-chains REVERT: C 43 LYS cc_start: 0.6853 (OUTLIER) cc_final: 0.6234 (tttm) REVERT: C 105 LYS cc_start: 0.2829 (OUTLIER) cc_final: -0.0047 (tttp) REVERT: C 106 ASN cc_start: 0.5675 (OUTLIER) cc_final: 0.4581 (m-40) REVERT: C 112 LEU cc_start: 0.5804 (OUTLIER) cc_final: 0.5518 (mp) REVERT: A 193 MET cc_start: 0.6569 (OUTLIER) cc_final: 0.6247 (mpp) REVERT: A 224 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.5854 (tpm170) REVERT: A 359 PHE cc_start: 0.5742 (OUTLIER) cc_final: 0.4980 (m-80) REVERT: B 321 ASN cc_start: 0.4968 (OUTLIER) cc_final: 0.4491 (p0) REVERT: B 442 MET cc_start: 0.4548 (tpt) cc_final: 0.4342 (tpt) REVERT: B 505 ILE cc_start: 0.3869 (OUTLIER) cc_final: 0.2055 (tt) REVERT: B 621 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.5983 (mt) outliers start: 76 outliers final: 47 residues processed: 155 average time/residue: 0.3472 time to fit residues: 59.4327 Evaluate side-chains 136 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 79 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 29 CYS Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain G residue 343 GLN Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 648 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 106 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 116 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 62 optimal weight: 0.0970 chunk 31 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 212 GLN A 322 HIS B 91 GLN B 109 GLN ** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN B 323 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.249407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.224218 restraints weight = 12812.978| |-----------------------------------------------------------------------------| r_work (start): 0.4738 rms_B_bonded: 1.57 r_work: 0.4634 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.4525 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.4525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6260 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 10297 Z= 0.219 Angle : 0.728 15.590 14016 Z= 0.381 Chirality : 0.046 0.226 1583 Planarity : 0.005 0.070 1673 Dihedral : 17.321 134.383 1613 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.11 % Favored : 88.80 % Rotamer: Outliers : 7.61 % Allowed : 35.78 % Favored : 56.61 % 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: -2.38 (0.24), residues: 1134 helix: -0.68 (0.22), residues: 556 sheet: -2.15 (0.67), residues: 51 loop : -2.54 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 211 TYR 0.021 0.002 TYR A 232 PHE 0.046 0.002 PHE B 172 TRP 0.011 0.002 TRP B 641 HIS 0.006 0.002 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 (10297) covalent geometry : angle 0.72829 / 0.38 (14016) hydrogen bonds : bond 0.04516 / 3.00 ( 373) hydrogen bonds : angle 4.93962 / 3.38 ( 1080) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 82 time to evaluate : 0.326 Fit side-chains REVERT: C 43 LYS cc_start: 0.6958 (OUTLIER) cc_final: 0.6256 (tttm) REVERT: C 61 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7306 (mp) REVERT: C 105 LYS cc_start: 0.3036 (OUTLIER) cc_final: -0.0195 (tmtm) REVERT: C 106 ASN cc_start: 0.5886 (OUTLIER) cc_final: 0.4888 (m110) REVERT: C 112 LEU cc_start: 0.5777 (OUTLIER) cc_final: 0.5443 (mp) REVERT: A 155 ARG cc_start: 0.6066 (OUTLIER) cc_final: 0.5756 (pmt-80) REVERT: A 193 MET cc_start: 0.6558 (OUTLIER) cc_final: 0.6197 (mpp) REVERT: A 224 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.5614 (tpm170) REVERT: A 359 PHE cc_start: 0.5960 (OUTLIER) cc_final: 0.5096 (m-80) REVERT: B 321 ASN cc_start: 0.5005 (OUTLIER) cc_final: 0.4411 (p0) REVERT: B 372 LEU cc_start: 0.3924 (OUTLIER) cc_final: 0.3530 (pp) REVERT: B 505 ILE cc_start: 0.4035 (OUTLIER) cc_final: 0.2356 (tt) REVERT: B 621 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6033 (mt) outliers start: 80 outliers final: 48 residues processed: 156 average time/residue: 0.3123 time to fit residues: 54.8533 Evaluate side-chains 140 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 79 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 29 CYS Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 343 GLN Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 648 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 82 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 4 optimal weight: 0.1980 chunk 20 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 ASN A 212 GLN ** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.252029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.227485 restraints weight = 12799.716| |-----------------------------------------------------------------------------| r_work (start): 0.4768 rms_B_bonded: 1.55 r_work: 0.4665 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.4554 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.4554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6188 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10297 Z= 0.151 Angle : 0.664 14.470 14016 Z= 0.348 Chirality : 0.044 0.218 1583 Planarity : 0.004 0.046 1673 Dihedral : 17.273 133.438 1613 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.93 % Favored : 88.98 % Rotamer: Outliers : 7.04 % Allowed : 37.11 % Favored : 55.85 % 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: -2.24 (0.25), residues: 1134 helix: -0.55 (0.22), residues: 557 sheet: -2.27 (0.66), residues: 52 loop : -2.47 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 297 TYR 0.017 0.001 TYR C 31 PHE 0.030 0.002 PHE B 172 TRP 0.013 0.002 TRP B 641 HIS 0.005 0.001 HIS B 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (10297) covalent geometry : angle 0.66395 / 0.35 (14016) hydrogen bonds : bond 0.03956 / 2.65 ( 373) hydrogen bonds : angle 4.79207 / 3.28 ( 1080) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 84 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: C 43 LYS cc_start: 0.6876 (OUTLIER) cc_final: 0.6231 (tttm) REVERT: C 105 LYS cc_start: 0.2911 (OUTLIER) cc_final: -0.0174 (tmtm) REVERT: C 106 ASN cc_start: 0.5682 (OUTLIER) cc_final: 0.4663 (m-40) REVERT: C 112 LEU cc_start: 0.5804 (OUTLIER) cc_final: 0.5493 (mp) REVERT: A 193 MET cc_start: 0.6589 (OUTLIER) cc_final: 0.6236 (mpp) REVERT: A 224 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.5629 (tpm170) REVERT: A 359 PHE cc_start: 0.5847 (OUTLIER) cc_final: 0.5006 (m-80) REVERT: B 321 ASN cc_start: 0.4980 (OUTLIER) cc_final: 0.4410 (p0) REVERT: B 372 LEU cc_start: 0.3919 (OUTLIER) cc_final: 0.3481 (pp) REVERT: B 505 ILE cc_start: 0.3865 (OUTLIER) cc_final: 0.2158 (tt) REVERT: B 621 LEU cc_start: 0.6571 (OUTLIER) cc_final: 0.6088 (mt) outliers start: 74 outliers final: 46 residues processed: 151 average time/residue: 0.2982 time to fit residues: 50.6772 Evaluate side-chains 140 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 83 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 29 CYS Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain G residue 303 LEU Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 343 GLN Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 648 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 20 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 ASN ** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4953 r_free = 0.4953 target = 0.251330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.226676 restraints weight = 12648.868| |-----------------------------------------------------------------------------| r_work (start): 0.4760 rms_B_bonded: 1.55 r_work: 0.4657 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.4547 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.4547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10297 Z= 0.169 Angle : 0.687 14.540 14016 Z= 0.359 Chirality : 0.045 0.223 1583 Planarity : 0.004 0.041 1673 Dihedral : 17.271 132.773 1613 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.20 % Favored : 88.62 % Rotamer: Outliers : 6.57 % Allowed : 37.39 % Favored : 56.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.28 (0.25), residues: 1134 helix: -0.61 (0.22), residues: 562 sheet: -2.32 (0.65), residues: 52 loop : -2.46 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 297 TYR 0.016 0.001 TYR A 232 PHE 0.032 0.002 PHE B 172 TRP 0.012 0.002 TRP B 641 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (10297) covalent geometry : angle 0.68701 / 0.36 (14016) hydrogen bonds : bond 0.04027 / 2.70 ( 373) hydrogen bonds : angle 4.80753 / 3.29 ( 1080) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 89 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 43 LYS cc_start: 0.6902 (OUTLIER) cc_final: 0.6240 (tttm) REVERT: C 105 LYS cc_start: 0.2979 (OUTLIER) cc_final: -0.0210 (tmtm) REVERT: C 106 ASN cc_start: 0.5717 (OUTLIER) cc_final: 0.4802 (m-40) REVERT: C 112 LEU cc_start: 0.5776 (OUTLIER) cc_final: 0.5463 (mp) REVERT: A 193 MET cc_start: 0.6692 (OUTLIER) cc_final: 0.6324 (mpp) REVERT: A 219 LYS cc_start: 0.7695 (tmmt) cc_final: 0.6951 (tttp) REVERT: A 224 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.5642 (tpm170) REVERT: A 359 PHE cc_start: 0.5861 (OUTLIER) cc_final: 0.5007 (m-80) REVERT: B 209 LEU cc_start: 0.6162 (mt) cc_final: 0.5777 (mp) REVERT: B 321 ASN cc_start: 0.5026 (OUTLIER) cc_final: 0.4409 (p0) REVERT: B 372 LEU cc_start: 0.3887 (OUTLIER) cc_final: 0.3446 (pp) REVERT: B 505 ILE cc_start: 0.3794 (OUTLIER) cc_final: 0.2072 (tt) REVERT: B 621 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6066 (mt) outliers start: 69 outliers final: 48 residues processed: 151 average time/residue: 0.3415 time to fit residues: 57.6136 Evaluate side-chains 145 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 86 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 29 CYS Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain G residue 303 LEU Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 343 GLN Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain G residue 370 SER Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 648 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 110 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.247807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.222500 restraints weight = 12844.610| |-----------------------------------------------------------------------------| r_work (start): 0.4725 rms_B_bonded: 1.57 r_work: 0.4620 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.4508 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.4508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 10297 Z= 0.228 Angle : 0.756 13.713 14016 Z= 0.395 Chirality : 0.047 0.230 1583 Planarity : 0.005 0.083 1673 Dihedral : 17.378 132.108 1613 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.99 % Favored : 87.92 % Rotamer: Outliers : 6.76 % Allowed : 37.20 % Favored : 56.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.45 (0.25), residues: 1134 helix: -0.78 (0.22), residues: 559 sheet: -2.19 (0.65), residues: 51 loop : -2.53 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 297 TYR 0.020 0.002 TYR A 232 PHE 0.033 0.002 PHE B 172 TRP 0.011 0.002 TRP B 641 HIS 0.007 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.23 (10297) covalent geometry : angle 0.75551 / 0.39 (14016) hydrogen bonds : bond 0.04548 / 3.01 ( 373) hydrogen bonds : angle 5.05124 / 3.46 ( 1080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3277.59 seconds wall clock time: 56 minutes 42.99 seconds (3402.99 seconds total)