Starting phenix.real_space_refine on Fri Aug 22 17:37:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aqv_15591/08_2025/8aqv_15591.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aqv_15591/08_2025/8aqv_15591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8aqv_15591/08_2025/8aqv_15591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aqv_15591/08_2025/8aqv_15591.map" model { file = "/net/cci-nas-00/data/ceres_data/8aqv_15591/08_2025/8aqv_15591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aqv_15591/08_2025/8aqv_15591.cif" } resolution = 2.96 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= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4117 2.51 5 N 1080 2.21 5 O 1213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6447 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4858 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "B" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1547 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 11, 'TRANS': 181} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.25, per 1000 atoms: 0.19 Number of scatterers: 6447 At special positions: 0 Unit cell: (88.2528, 87.2384, 119.699, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1213 8.00 N 1080 7.00 C 4117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG B1301 " - " ASN B 343 " " NAG C 1 " - " ASN A 53 " Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 344.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 7 sheets defined 53.2% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 21 through 40 removed outlier: 3.816A pdb=" N LYS A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 35 " --> pdb=" O ASN A 31 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 52 removed outlier: 3.506A pdb=" N SER A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 80 removed outlier: 3.686A pdb=" N LYS A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 removed outlier: 3.610A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 176 removed outlier: 3.606A pdb=" N ALA A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LYS A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.590A pdb=" N TYR A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 208 removed outlier: 3.895A pdb=" N GLU A 208 " --> pdb=" O GLY A 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 205 through 208' Processing helix chain 'A' and resid 220 through 233 removed outlier: 4.579A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 230 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.822A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.534A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.544A pdb=" N GLY A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 311 removed outlier: 3.637A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.531A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 329 removed outlier: 4.024A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 324 through 329' Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.620A pdb=" N ALA A 372 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 402 through 413 removed outlier: 4.107A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.617A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 421' Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.746A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 472 through 485 removed outlier: 3.802A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.969A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.834A pdb=" N LYS A 541 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 538 through 542' Processing helix chain 'A' and resid 551 through 559 removed outlier: 3.504A pdb=" N LEU A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.824A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.532A pdb=" N TYR A 587 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.693A pdb=" N ASP A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.917A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.754A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.701A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.715A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 209 through 210 removed outlier: 3.822A pdb=" N ALA A 209 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.960A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.241A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'B' and resid 473 through 474 252 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.93 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2067 1.34 - 1.46: 1512 1.46 - 1.58: 2992 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6629 Sorted by residual: bond pdb=" C ALA B 372 " pdb=" N PRO B 373 " ideal model delta sigma weight residual 1.333 1.374 -0.041 1.01e-02 9.80e+03 1.64e+01 bond pdb=" C GLU A 145 " pdb=" N PRO A 146 " ideal model delta sigma weight residual 1.331 1.347 -0.015 7.90e-03 1.60e+04 3.75e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C TYR A 279 " pdb=" N PRO A 280 " ideal model delta sigma weight residual 1.335 1.354 -0.018 1.36e-02 5.41e+03 1.85e+00 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.30e+00 ... (remaining 6624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 8751 1.85 - 3.71: 218 3.71 - 5.56: 29 5.56 - 7.42: 5 7.42 - 9.27: 2 Bond angle restraints: 9005 Sorted by residual: angle pdb=" C ASP A 338 " pdb=" CA ASP A 338 " pdb=" CB ASP A 338 " ideal model delta sigma weight residual 116.54 110.34 6.20 1.15e+00 7.56e-01 2.90e+01 angle pdb=" N VAL B 341 " pdb=" CA VAL B 341 " pdb=" C VAL B 341 " ideal model delta sigma weight residual 113.71 108.69 5.02 9.50e-01 1.11e+00 2.80e+01 angle pdb=" N GLU A 483 " pdb=" CA GLU A 483 " pdb=" C GLU A 483 " ideal model delta sigma weight residual 114.75 109.32 5.43 1.26e+00 6.30e-01 1.85e+01 angle pdb=" N THR B 523 " pdb=" CA THR B 523 " pdb=" C THR B 523 " ideal model delta sigma weight residual 114.56 109.14 5.42 1.27e+00 6.20e-01 1.82e+01 angle pdb=" C PHE B 371 " pdb=" N ALA B 372 " pdb=" CA ALA B 372 " ideal model delta sigma weight residual 121.80 131.07 -9.27 2.44e+00 1.68e-01 1.44e+01 ... (remaining 9000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 3633 17.79 - 35.58: 266 35.58 - 53.37: 38 53.37 - 71.16: 18 71.16 - 88.96: 5 Dihedral angle restraints: 3960 sinusoidal: 1639 harmonic: 2321 Sorted by residual: dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -145.69 59.69 1 1.00e+01 1.00e-02 4.76e+01 dihedral pdb=" CA GLN A 86 " pdb=" C GLN A 86 " pdb=" N GLU A 87 " pdb=" CA GLU A 87 " ideal model delta harmonic sigma weight residual 180.00 151.13 28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA GLU A 87 " pdb=" C GLU A 87 " pdb=" N ILE A 88 " pdb=" CA ILE A 88 " ideal model delta harmonic sigma weight residual 180.00 162.07 17.93 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 3957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 488 0.027 - 0.054: 276 0.054 - 0.080: 116 0.080 - 0.107: 44 0.107 - 0.134: 17 Chirality restraints: 941 Sorted by residual: chirality pdb=" CA ILE B 434 " pdb=" N ILE B 434 " pdb=" C ILE B 434 " pdb=" CB ILE B 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CB THR A 55 " pdb=" CA THR A 55 " pdb=" OG1 THR A 55 " pdb=" CG2 THR A 55 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 ... (remaining 938 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 336 " -0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO B 337 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 337 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 337 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 88 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C ILE A 88 " -0.024 2.00e-02 2.50e+03 pdb=" O ILE A 88 " 0.009 2.00e-02 2.50e+03 pdb=" N GLN A 89 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO A 235 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " -0.019 5.00e-02 4.00e+02 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 190 2.71 - 3.26: 6126 3.26 - 3.81: 9501 3.81 - 4.35: 12542 4.35 - 4.90: 21501 Nonbonded interactions: 49860 Sorted by model distance: nonbonded pdb=" NH2 ARG A 245 " pdb=" O PHE A 603 " model vdw 2.164 3.120 nonbonded pdb=" NH2 ARG B 454 " pdb=" O SER B 469 " model vdw 2.213 3.120 nonbonded pdb=" O THR A 548 " pdb=" NE2 GLN A 552 " model vdw 2.229 3.120 nonbonded pdb=" OE2 GLU A 227 " pdb=" OH TYR A 454 " model vdw 2.281 3.040 nonbonded pdb=" NE ARG B 457 " pdb=" OD2 ASP B 467 " model vdw 2.296 3.120 ... (remaining 49855 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: 2.660 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.030 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:6.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 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 : 0.003 0.041 6639 Z= 0.177 Angle : 0.712 9.272 9028 Z= 0.430 Chirality : 0.042 0.134 941 Planarity : 0.004 0.047 1168 Dihedral : 12.963 88.956 2449 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.64 % Allowed : 4.84 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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 aren not related in a simple way. whole: -1.32 (0.30), residues: 785 helix: -0.39 (0.29), residues: 348 sheet: 0.24 (0.86), residues: 43 loop : -1.42 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 518 TYR 0.022 0.002 TYR B 501 PHE 0.016 0.001 PHE A 369 TRP 0.011 0.001 TRP A 165 HIS 0.007 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6629) covalent geometry : angle 0.70970 ( 9005) SS BOND : bond 0.00643 ( 7) SS BOND : angle 0.75382 ( 14) hydrogen bonds : bond 0.20732 ( 252) hydrogen bonds : angle 7.26316 ( 705) link_BETA1-4 : bond 0.00798 ( 1) link_BETA1-4 : angle 1.83216 ( 3) link_NAG-ASN : bond 0.00295 ( 2) link_NAG-ASN : angle 2.16583 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 298 MET cc_start: 0.8589 (mtt) cc_final: 0.8339 (mtp) REVERT: A 508 ASN cc_start: 0.8108 (m110) cc_final: 0.7833 (m-40) REVERT: B 357 ARG cc_start: 0.8523 (ttp80) cc_final: 0.7971 (ttt90) REVERT: B 405 ASN cc_start: 0.7716 (m-40) cc_final: 0.7467 (m110) REVERT: B 440 LYS cc_start: 0.8887 (mmtp) cc_final: 0.8509 (mtpm) REVERT: B 469 SER cc_start: 0.8236 (t) cc_final: 0.7994 (p) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.5289 time to fit residues: 69.8150 Evaluate side-chains 76 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 81 GLN A 102 GLN A 121 ASN A 188 ASN A 330 ASN A 368 ASN A 397 ASN A 522 GLN A 540 HIS B 388 ASN B 450 ASN B 487 ASN B 506 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.177739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.123420 restraints weight = 7661.054| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.44 r_work: 0.3273 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6639 Z= 0.141 Angle : 0.589 10.167 9028 Z= 0.304 Chirality : 0.042 0.141 941 Planarity : 0.005 0.046 1168 Dihedral : 4.205 26.662 927 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.64 % Allowed : 4.97 % Favored : 94.39 % Rotamer: Outliers : 2.48 % Allowed : 9.04 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.30), residues: 785 helix: 0.12 (0.29), residues: 357 sheet: 0.56 (0.85), residues: 43 loop : -1.35 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 192 TYR 0.023 0.001 TYR A 255 PHE 0.017 0.001 PHE A 369 TRP 0.013 0.001 TRP A 477 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6629) covalent geometry : angle 0.58466 ( 9005) SS BOND : bond 0.00509 ( 7) SS BOND : angle 1.02481 ( 14) hydrogen bonds : bond 0.05174 ( 252) hydrogen bonds : angle 5.00452 ( 705) link_BETA1-4 : bond 0.00337 ( 1) link_BETA1-4 : angle 1.05004 ( 3) link_NAG-ASN : bond 0.00283 ( 2) link_NAG-ASN : angle 2.30459 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 89 GLN cc_start: 0.6821 (OUTLIER) cc_final: 0.5925 (mt0) REVERT: A 298 MET cc_start: 0.8451 (mtt) cc_final: 0.8173 (mtp) REVERT: A 439 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6956 (mp) REVERT: B 357 ARG cc_start: 0.8688 (ttp80) cc_final: 0.8137 (ttt90) REVERT: B 378 LYS cc_start: 0.7633 (tptp) cc_final: 0.7389 (mmmt) REVERT: B 405 ASN cc_start: 0.7938 (m-40) cc_final: 0.7727 (m110) REVERT: B 440 LYS cc_start: 0.8993 (mmtp) cc_final: 0.8674 (mtpm) REVERT: B 458 LYS cc_start: 0.7679 (pttt) cc_final: 0.7469 (ptpp) outliers start: 17 outliers final: 5 residues processed: 93 average time/residue: 0.5635 time to fit residues: 55.0438 Evaluate side-chains 80 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 549 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 71 optimal weight: 0.9980 chunk 30 optimal weight: 0.0170 chunk 21 optimal weight: 0.0770 chunk 42 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 64 optimal weight: 0.0770 chunk 37 optimal weight: 0.3980 chunk 62 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 overall best weight: 0.2734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 175 GLN A 536 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.180770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.127319 restraints weight = 7666.792| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.45 r_work: 0.3291 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6639 Z= 0.094 Angle : 0.514 10.620 9028 Z= 0.261 Chirality : 0.040 0.143 941 Planarity : 0.004 0.043 1168 Dihedral : 3.820 25.857 927 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.64 % Allowed : 4.97 % Favored : 94.39 % Rotamer: Outliers : 2.33 % Allowed : 10.79 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.30), residues: 785 helix: 0.43 (0.29), residues: 358 sheet: 0.62 (0.85), residues: 43 loop : -1.25 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.018 0.001 TYR A 255 PHE 0.010 0.001 PHE A 369 TRP 0.011 0.001 TRP A 477 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00191 ( 6629) covalent geometry : angle 0.50875 ( 9005) SS BOND : bond 0.00445 ( 7) SS BOND : angle 1.30283 ( 14) hydrogen bonds : bond 0.03616 ( 252) hydrogen bonds : angle 4.59456 ( 705) link_BETA1-4 : bond 0.00476 ( 1) link_BETA1-4 : angle 0.93462 ( 3) link_NAG-ASN : bond 0.00206 ( 2) link_NAG-ASN : angle 2.08116 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7549 (tt0) cc_final: 0.7146 (tm-30) REVERT: A 89 GLN cc_start: 0.6336 (OUTLIER) cc_final: 0.5548 (mt0) REVERT: A 102 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7775 (mm-40) REVERT: A 298 MET cc_start: 0.8438 (mtt) cc_final: 0.8206 (mtp) REVERT: A 607 ASN cc_start: 0.4775 (t0) cc_final: 0.4541 (t0) REVERT: B 357 ARG cc_start: 0.8652 (ttp80) cc_final: 0.8226 (ttt90) REVERT: B 405 ASN cc_start: 0.7831 (m-40) cc_final: 0.7597 (m110) REVERT: B 440 LYS cc_start: 0.8994 (mmtp) cc_final: 0.8664 (mtpm) REVERT: B 458 LYS cc_start: 0.7438 (pttt) cc_final: 0.7194 (ptpp) REVERT: B 471 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7416 (mt-10) outliers start: 16 outliers final: 4 residues processed: 88 average time/residue: 0.5357 time to fit residues: 49.5518 Evaluate side-chains 81 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 501 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 59 optimal weight: 0.0170 chunk 50 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 32 optimal weight: 0.0980 chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.176922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.122128 restraints weight = 7596.829| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.45 r_work: 0.3222 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6639 Z= 0.126 Angle : 0.542 10.338 9028 Z= 0.275 Chirality : 0.041 0.139 941 Planarity : 0.004 0.041 1168 Dihedral : 3.874 25.803 927 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.84 % Favored : 94.65 % Rotamer: Outliers : 2.62 % Allowed : 11.22 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.30), residues: 785 helix: 0.49 (0.29), residues: 362 sheet: 0.64 (0.83), residues: 43 loop : -1.18 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 246 TYR 0.019 0.001 TYR A 255 PHE 0.013 0.001 PHE A 369 TRP 0.011 0.001 TRP A 477 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 6629) covalent geometry : angle 0.53761 ( 9005) SS BOND : bond 0.00485 ( 7) SS BOND : angle 0.82012 ( 14) hydrogen bonds : bond 0.04166 ( 252) hydrogen bonds : angle 4.52640 ( 705) link_BETA1-4 : bond 0.00506 ( 1) link_BETA1-4 : angle 1.17028 ( 3) link_NAG-ASN : bond 0.00262 ( 2) link_NAG-ASN : angle 2.28407 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 89 GLN cc_start: 0.6473 (OUTLIER) cc_final: 0.5631 (mt0) REVERT: A 102 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7669 (mm-40) REVERT: A 246 ARG cc_start: 0.7290 (ttm-80) cc_final: 0.6974 (mtm-85) REVERT: A 298 MET cc_start: 0.8433 (mtt) cc_final: 0.8202 (mtp) REVERT: A 607 ASN cc_start: 0.4791 (t0) cc_final: 0.4578 (t0) REVERT: B 357 ARG cc_start: 0.8684 (ttp80) cc_final: 0.8255 (ttt90) REVERT: B 405 ASN cc_start: 0.7956 (m-40) cc_final: 0.7643 (m-40) REVERT: B 458 LYS cc_start: 0.7577 (pttt) cc_final: 0.7311 (ptpp) outliers start: 18 outliers final: 10 residues processed: 85 average time/residue: 0.5273 time to fit residues: 47.3137 Evaluate side-chains 82 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 12 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 26 optimal weight: 0.0000 chunk 10 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS B 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.176951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.122546 restraints weight = 7735.984| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.40 r_work: 0.3259 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6639 Z= 0.118 Angle : 0.544 10.541 9028 Z= 0.274 Chirality : 0.041 0.177 941 Planarity : 0.004 0.039 1168 Dihedral : 3.881 25.561 927 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.84 % Favored : 94.65 % Rotamer: Outliers : 3.35 % Allowed : 11.22 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.31), residues: 785 helix: 0.58 (0.29), residues: 361 sheet: 0.48 (0.84), residues: 43 loop : -1.10 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 246 TYR 0.018 0.001 TYR A 255 PHE 0.011 0.001 PHE A 369 TRP 0.011 0.001 TRP A 477 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6629) covalent geometry : angle 0.53578 ( 9005) SS BOND : bond 0.00673 ( 7) SS BOND : angle 1.80737 ( 14) hydrogen bonds : bond 0.03837 ( 252) hydrogen bonds : angle 4.45620 ( 705) link_BETA1-4 : bond 0.00339 ( 1) link_BETA1-4 : angle 1.13813 ( 3) link_NAG-ASN : bond 0.00304 ( 2) link_NAG-ASN : angle 2.37285 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7587 (tt0) cc_final: 0.7174 (tm-30) REVERT: A 89 GLN cc_start: 0.6418 (OUTLIER) cc_final: 0.5611 (mt0) REVERT: A 102 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7757 (mm-40) REVERT: A 298 MET cc_start: 0.8410 (mtt) cc_final: 0.8182 (mtp) REVERT: A 607 ASN cc_start: 0.4800 (t0) cc_final: 0.4588 (t0) REVERT: B 346 ARG cc_start: 0.7870 (mmt180) cc_final: 0.7426 (ptm160) REVERT: B 357 ARG cc_start: 0.8647 (ttp80) cc_final: 0.8237 (ttt90) REVERT: B 405 ASN cc_start: 0.7934 (m-40) cc_final: 0.7600 (m-40) REVERT: B 458 LYS cc_start: 0.7422 (pttt) cc_final: 0.7156 (ptpp) outliers start: 23 outliers final: 8 residues processed: 89 average time/residue: 0.4723 time to fit residues: 44.4062 Evaluate side-chains 78 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 25 optimal weight: 0.0070 chunk 66 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS A 401 HIS B 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.175250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.120645 restraints weight = 7723.621| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.42 r_work: 0.3228 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6639 Z= 0.139 Angle : 0.561 10.494 9028 Z= 0.283 Chirality : 0.042 0.170 941 Planarity : 0.004 0.037 1168 Dihedral : 3.959 25.644 927 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.48 % Favored : 94.01 % Rotamer: Outliers : 2.77 % Allowed : 11.66 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.30), residues: 785 helix: 0.60 (0.29), residues: 362 sheet: 0.73 (0.83), residues: 43 loop : -1.08 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 246 TYR 0.019 0.001 TYR A 243 PHE 0.011 0.001 PHE A 369 TRP 0.011 0.001 TRP A 477 HIS 0.006 0.002 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 6629) covalent geometry : angle 0.55633 ( 9005) SS BOND : bond 0.00690 ( 7) SS BOND : angle 1.03206 ( 14) hydrogen bonds : bond 0.04249 ( 252) hydrogen bonds : angle 4.47870 ( 705) link_BETA1-4 : bond 0.00521 ( 1) link_BETA1-4 : angle 1.27319 ( 3) link_NAG-ASN : bond 0.00320 ( 2) link_NAG-ASN : angle 2.53830 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.268 Fit side-chains REVERT: A 75 GLU cc_start: 0.7667 (tt0) cc_final: 0.7265 (tm-30) REVERT: A 89 GLN cc_start: 0.6579 (OUTLIER) cc_final: 0.5700 (mt0) REVERT: A 102 GLN cc_start: 0.7968 (mm-40) cc_final: 0.7647 (mm-40) REVERT: A 219 ARG cc_start: 0.6363 (ptt-90) cc_final: 0.6048 (ptt-90) REVERT: A 298 MET cc_start: 0.8394 (mtt) cc_final: 0.8143 (mtp) REVERT: A 607 ASN cc_start: 0.4897 (t0) cc_final: 0.4687 (t0) REVERT: B 346 ARG cc_start: 0.7997 (mmt180) cc_final: 0.7431 (ptm160) REVERT: B 357 ARG cc_start: 0.8767 (ttp80) cc_final: 0.8481 (ttp80) REVERT: B 405 ASN cc_start: 0.8070 (m-40) cc_final: 0.7751 (m-40) REVERT: B 458 LYS cc_start: 0.7471 (pttt) cc_final: 0.7230 (ptpp) REVERT: B 471 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7471 (mt-10) outliers start: 19 outliers final: 10 residues processed: 83 average time/residue: 0.5192 time to fit residues: 45.6088 Evaluate side-chains 79 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.0470 chunk 52 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS A 401 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.177128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.123561 restraints weight = 7623.761| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.34 r_work: 0.3267 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6639 Z= 0.110 Angle : 0.534 10.658 9028 Z= 0.268 Chirality : 0.041 0.185 941 Planarity : 0.004 0.036 1168 Dihedral : 3.852 25.329 927 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.22 % Favored : 94.39 % Rotamer: Outliers : 2.92 % Allowed : 11.52 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.31), residues: 785 helix: 0.83 (0.29), residues: 353 sheet: 0.64 (0.84), residues: 43 loop : -1.10 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 454 TYR 0.017 0.001 TYR A 255 PHE 0.010 0.001 PHE A 369 TRP 0.011 0.001 TRP A 477 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 6629) covalent geometry : angle 0.52811 ( 9005) SS BOND : bond 0.00483 ( 7) SS BOND : angle 1.22676 ( 14) hydrogen bonds : bond 0.03680 ( 252) hydrogen bonds : angle 4.41939 ( 705) link_BETA1-4 : bond 0.00563 ( 1) link_BETA1-4 : angle 1.18059 ( 3) link_NAG-ASN : bond 0.00284 ( 2) link_NAG-ASN : angle 2.45114 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7531 (tt0) cc_final: 0.7120 (tm-30) REVERT: A 89 GLN cc_start: 0.6333 (OUTLIER) cc_final: 0.5542 (mt0) REVERT: A 102 GLN cc_start: 0.7910 (mm-40) cc_final: 0.7663 (mm-40) REVERT: A 208 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8136 (tm-30) REVERT: A 255 TYR cc_start: 0.6539 (OUTLIER) cc_final: 0.4560 (t80) REVERT: A 298 MET cc_start: 0.8323 (mtt) cc_final: 0.8085 (mtp) REVERT: A 607 ASN cc_start: 0.4825 (t0) cc_final: 0.4608 (t0) REVERT: B 346 ARG cc_start: 0.7984 (mmt180) cc_final: 0.7318 (ptm160) REVERT: B 357 ARG cc_start: 0.8642 (ttp80) cc_final: 0.8335 (ttp80) REVERT: B 405 ASN cc_start: 0.8005 (m-40) cc_final: 0.7660 (m-40) REVERT: B 458 LYS cc_start: 0.7364 (pttt) cc_final: 0.7067 (ptpp) REVERT: B 471 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7459 (mt-10) outliers start: 20 outliers final: 8 residues processed: 86 average time/residue: 0.5063 time to fit residues: 46.0403 Evaluate side-chains 80 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 0.0570 chunk 60 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS A 401 HIS ** A 540 HIS ** 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 = 0.4014 r_free = 0.4014 target = 0.178723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125815 restraints weight = 7607.438| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.30 r_work: 0.3289 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6639 Z= 0.101 Angle : 0.527 10.684 9028 Z= 0.262 Chirality : 0.040 0.160 941 Planarity : 0.004 0.036 1168 Dihedral : 3.749 25.061 927 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.48 % Favored : 94.14 % Rotamer: Outliers : 2.33 % Allowed : 12.83 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.31), residues: 785 helix: 0.94 (0.29), residues: 349 sheet: 0.72 (0.84), residues: 43 loop : -1.05 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.017 0.001 TYR A 255 PHE 0.009 0.001 PHE A 369 TRP 0.011 0.001 TRP A 477 HIS 0.008 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 6629) covalent geometry : angle 0.52256 ( 9005) SS BOND : bond 0.00603 ( 7) SS BOND : angle 0.94063 ( 14) hydrogen bonds : bond 0.03476 ( 252) hydrogen bonds : angle 4.37292 ( 705) link_BETA1-4 : bond 0.00539 ( 1) link_BETA1-4 : angle 1.16046 ( 3) link_NAG-ASN : bond 0.00222 ( 2) link_NAG-ASN : angle 2.37050 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7540 (tt0) cc_final: 0.7136 (tm-30) REVERT: A 89 GLN cc_start: 0.6289 (OUTLIER) cc_final: 0.5550 (mt0) REVERT: A 102 GLN cc_start: 0.7918 (mm-40) cc_final: 0.7577 (mm-40) REVERT: A 208 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8114 (tm-30) REVERT: A 255 TYR cc_start: 0.6476 (OUTLIER) cc_final: 0.4436 (t80) REVERT: A 298 MET cc_start: 0.8360 (mtt) cc_final: 0.8140 (mtp) REVERT: A 607 ASN cc_start: 0.4911 (t0) cc_final: 0.4702 (t0) REVERT: B 346 ARG cc_start: 0.8005 (mmt180) cc_final: 0.7345 (ptm160) REVERT: B 357 ARG cc_start: 0.8602 (ttp80) cc_final: 0.8219 (ttt90) REVERT: B 405 ASN cc_start: 0.7986 (m-40) cc_final: 0.7648 (m-40) REVERT: B 458 LYS cc_start: 0.7295 (pttt) cc_final: 0.7012 (ptpp) REVERT: B 471 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7360 (mt-10) outliers start: 16 outliers final: 9 residues processed: 80 average time/residue: 0.5537 time to fit residues: 46.6566 Evaluate side-chains 77 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 71 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 22 optimal weight: 0.6980 chunk 67 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.177124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.123802 restraints weight = 7707.713| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.33 r_work: 0.3282 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6639 Z= 0.110 Angle : 0.540 10.629 9028 Z= 0.268 Chirality : 0.041 0.159 941 Planarity : 0.004 0.036 1168 Dihedral : 3.776 25.081 927 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.35 % Favored : 94.39 % Rotamer: Outliers : 2.48 % Allowed : 13.27 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.31), residues: 785 helix: 1.00 (0.29), residues: 349 sheet: 0.78 (0.85), residues: 43 loop : -1.00 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 518 TYR 0.017 0.001 TYR A 255 PHE 0.010 0.001 PHE A 369 TRP 0.011 0.001 TRP A 477 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 6629) covalent geometry : angle 0.53521 ( 9005) SS BOND : bond 0.00608 ( 7) SS BOND : angle 0.91062 ( 14) hydrogen bonds : bond 0.03619 ( 252) hydrogen bonds : angle 4.36940 ( 705) link_BETA1-4 : bond 0.00516 ( 1) link_BETA1-4 : angle 1.17693 ( 3) link_NAG-ASN : bond 0.00238 ( 2) link_NAG-ASN : angle 2.40548 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7603 (tt0) cc_final: 0.7205 (tm-30) REVERT: A 89 GLN cc_start: 0.6336 (OUTLIER) cc_final: 0.5619 (mt0) REVERT: A 102 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7619 (mm-40) REVERT: A 208 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8235 (tm-30) REVERT: A 255 TYR cc_start: 0.6453 (OUTLIER) cc_final: 0.4346 (t80) REVERT: A 298 MET cc_start: 0.8354 (mtt) cc_final: 0.8129 (mtp) REVERT: A 595 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6380 (mm) REVERT: A 607 ASN cc_start: 0.4924 (t0) cc_final: 0.4716 (t0) REVERT: B 346 ARG cc_start: 0.8023 (mmt180) cc_final: 0.7398 (ptm160) REVERT: B 357 ARG cc_start: 0.8647 (ttp80) cc_final: 0.8277 (ttt90) REVERT: B 405 ASN cc_start: 0.7989 (m-40) cc_final: 0.7672 (m-40) REVERT: B 458 LYS cc_start: 0.7260 (pttt) cc_final: 0.7004 (ptpp) REVERT: B 471 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7380 (mt-10) outliers start: 17 outliers final: 9 residues processed: 81 average time/residue: 0.6086 time to fit residues: 51.9841 Evaluate side-chains 79 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 0.0030 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS A 401 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.174945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.132454 restraints weight = 7566.870| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.78 r_work: 0.3185 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6639 Z= 0.145 Angle : 0.578 10.524 9028 Z= 0.288 Chirality : 0.042 0.176 941 Planarity : 0.004 0.035 1168 Dihedral : 3.967 25.278 927 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.48 % Favored : 94.27 % Rotamer: Outliers : 2.48 % Allowed : 13.41 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.31), residues: 785 helix: 0.90 (0.29), residues: 353 sheet: 0.93 (0.86), residues: 43 loop : -1.04 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 518 TYR 0.018 0.001 TYR A 255 PHE 0.012 0.001 PHE A 369 TRP 0.011 0.001 TRP A 477 HIS 0.008 0.002 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 6629) covalent geometry : angle 0.57333 ( 9005) SS BOND : bond 0.00746 ( 7) SS BOND : angle 1.01966 ( 14) hydrogen bonds : bond 0.04171 ( 252) hydrogen bonds : angle 4.46233 ( 705) link_BETA1-4 : bond 0.00500 ( 1) link_BETA1-4 : angle 1.24907 ( 3) link_NAG-ASN : bond 0.00329 ( 2) link_NAG-ASN : angle 2.62208 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7674 (tt0) cc_final: 0.7255 (tm-30) REVERT: A 89 GLN cc_start: 0.6433 (OUTLIER) cc_final: 0.5658 (mt0) REVERT: A 102 GLN cc_start: 0.7967 (mm-40) cc_final: 0.7719 (mm-40) REVERT: A 208 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8358 (tm-30) REVERT: A 210 GLU cc_start: 0.8098 (pt0) cc_final: 0.7504 (tp30) REVERT: A 255 TYR cc_start: 0.6533 (OUTLIER) cc_final: 0.4376 (t80) REVERT: A 298 MET cc_start: 0.8339 (mtt) cc_final: 0.8099 (mtp) REVERT: A 595 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6434 (mm) REVERT: A 607 ASN cc_start: 0.5006 (t0) cc_final: 0.4788 (t0) REVERT: B 346 ARG cc_start: 0.8033 (mmt180) cc_final: 0.7403 (ptm160) REVERT: B 357 ARG cc_start: 0.8720 (ttp80) cc_final: 0.8455 (ttp80) REVERT: B 405 ASN cc_start: 0.8055 (m-40) cc_final: 0.7790 (m-40) REVERT: B 458 LYS cc_start: 0.7436 (pttt) cc_final: 0.7085 (ptpt) REVERT: B 471 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7519 (mt-10) outliers start: 17 outliers final: 9 residues processed: 80 average time/residue: 0.5852 time to fit residues: 49.4448 Evaluate side-chains 79 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 68 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 chunk 54 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.177201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.126213 restraints weight = 7676.650| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.64 r_work: 0.3242 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6639 Z= 0.109 Angle : 0.541 10.737 9028 Z= 0.267 Chirality : 0.041 0.154 941 Planarity : 0.004 0.035 1168 Dihedral : 3.820 24.874 927 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.61 % Favored : 94.14 % Rotamer: Outliers : 2.19 % Allowed : 13.70 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.31), residues: 785 helix: 0.99 (0.29), residues: 352 sheet: 0.89 (0.85), residues: 43 loop : -1.00 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.017 0.001 TYR A 255 PHE 0.010 0.001 PHE A 369 TRP 0.011 0.001 TRP A 477 HIS 0.010 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 6629) covalent geometry : angle 0.53592 ( 9005) SS BOND : bond 0.00612 ( 7) SS BOND : angle 0.91924 ( 14) hydrogen bonds : bond 0.03577 ( 252) hydrogen bonds : angle 4.39175 ( 705) link_BETA1-4 : bond 0.00440 ( 1) link_BETA1-4 : angle 1.11337 ( 3) link_NAG-ASN : bond 0.00263 ( 2) link_NAG-ASN : angle 2.50619 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2701.98 seconds wall clock time: 46 minutes 37.98 seconds (2797.98 seconds total)