Starting phenix.real_space_refine on Thu Jul 24 18:05:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aqv_15591/07_2025/8aqv_15591.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aqv_15591/07_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_15591/07_2025/8aqv_15591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aqv_15591/07_2025/8aqv_15591.map" model { file = "/net/cci-nas-00/data/ceres_data/8aqv_15591/07_2025/8aqv_15591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aqv_15591/07_2025/8aqv_15591.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.53, per 1000 atoms: 0.70 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: 1.53 Conformation dependent library (CDL) restraints added in 915.6 milliseconds 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: 0.68 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: 1.57 Time building geometry restraints manager: 1.83 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: 1.980 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.430 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.700 ------------------------------------------------------------------------------- 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 : 4.53 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.30), 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 TRP 0.011 0.001 TRP A 165 HIS 0.007 0.001 HIS A 401 PHE 0.016 0.001 PHE A 369 TYR 0.022 0.002 TYR B 501 ARG 0.002 0.000 ARG A 518 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 2) link_NAG-ASN : angle 2.16583 ( 6) link_BETA1-4 : bond 0.00798 ( 1) link_BETA1-4 : angle 1.83216 ( 3) hydrogen bonds : bond 0.20732 ( 252) hydrogen bonds : angle 7.26316 ( 705) SS BOND : bond 0.00643 ( 7) SS BOND : angle 0.75382 ( 14) covalent geometry : bond 0.00334 ( 6629) covalent geometry : angle 0.70970 ( 9005) *********************** 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 : 0.722 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: 0.7827 (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: 1.2641 time to fit residues: 166.9940 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 : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.5980 chunk 59 optimal weight: 0.0980 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.177729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.123487 restraints weight = 7536.366| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.41 r_work: 0.3245 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6639 Z= 0.139 Angle : 0.584 10.260 9028 Z= 0.302 Chirality : 0.042 0.139 941 Planarity : 0.005 0.046 1168 Dihedral : 4.170 26.540 927 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.10 % Favored : 94.27 % Rotamer: Outliers : 2.19 % Allowed : 9.48 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.30), residues: 785 helix: 0.13 (0.29), residues: 357 sheet: 0.54 (0.85), residues: 43 loop : -1.36 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 477 HIS 0.006 0.001 HIS A 241 PHE 0.015 0.001 PHE A 369 TYR 0.022 0.001 TYR A 255 ARG 0.006 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 2) link_NAG-ASN : angle 2.31614 ( 6) link_BETA1-4 : bond 0.00322 ( 1) link_BETA1-4 : angle 1.14950 ( 3) hydrogen bonds : bond 0.04968 ( 252) hydrogen bonds : angle 4.97099 ( 705) SS BOND : bond 0.00504 ( 7) SS BOND : angle 1.06877 ( 14) covalent geometry : bond 0.00313 ( 6629) covalent geometry : angle 0.57998 ( 9005) *********************** 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: 15 poor density : 83 time to evaluate : 0.712 Fit side-chains revert: symmetry clash REVERT: A 89 GLN cc_start: 0.6687 (OUTLIER) cc_final: 0.5784 (mt0) REVERT: A 298 MET cc_start: 0.8406 (mtt) cc_final: 0.8135 (mtp) REVERT: A 439 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6782 (mp) REVERT: B 357 ARG cc_start: 0.8691 (ttp80) cc_final: 0.8268 (ttt90) REVERT: B 378 LYS cc_start: 0.7565 (tptp) cc_final: 0.7346 (mmmt) REVERT: B 405 ASN cc_start: 0.7949 (m-40) cc_final: 0.7716 (m110) REVERT: B 440 LYS cc_start: 0.8991 (mmtp) cc_final: 0.8666 (mtpm) REVERT: B 458 LYS cc_start: 0.7686 (pttt) cc_final: 0.7449 (ptpp) outliers start: 15 outliers final: 5 residues processed: 94 average time/residue: 1.3202 time to fit residues: 130.5748 Evaluate side-chains 81 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 39 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 chunk 42 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 216 ASN A 536 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.176548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.122403 restraints weight = 7661.623| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.44 r_work: 0.3227 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6639 Z= 0.127 Angle : 0.554 10.448 9028 Z= 0.282 Chirality : 0.042 0.165 941 Planarity : 0.004 0.042 1168 Dihedral : 4.035 26.103 927 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.64 % Allowed : 4.97 % Favored : 94.39 % Rotamer: Outliers : 2.19 % Allowed : 10.79 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.30), residues: 785 helix: 0.27 (0.29), residues: 363 sheet: 0.62 (0.85), residues: 43 loop : -1.27 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 477 HIS 0.006 0.001 HIS A 241 PHE 0.014 0.001 PHE A 369 TYR 0.017 0.001 TYR A 255 ARG 0.004 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 2) link_NAG-ASN : angle 2.31982 ( 6) link_BETA1-4 : bond 0.00426 ( 1) link_BETA1-4 : angle 1.10393 ( 3) hydrogen bonds : bond 0.04300 ( 252) hydrogen bonds : angle 4.65114 ( 705) SS BOND : bond 0.00717 ( 7) SS BOND : angle 1.41980 ( 14) covalent geometry : bond 0.00286 ( 6629) covalent geometry : angle 0.54824 ( 9005) *********************** 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 91 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 89 GLN cc_start: 0.6517 (OUTLIER) cc_final: 0.5663 (mt0) REVERT: A 102 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7721 (mm-40) REVERT: A 177 ARG cc_start: 0.6764 (tpt170) cc_final: 0.6554 (tpt90) REVERT: A 210 GLU cc_start: 0.8168 (tp30) cc_final: 0.7755 (tp30) REVERT: A 298 MET cc_start: 0.8403 (mtt) cc_final: 0.8143 (mtp) REVERT: A 439 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6795 (mp) REVERT: B 357 ARG cc_start: 0.8674 (ttp80) cc_final: 0.8244 (ttt90) REVERT: B 405 ASN cc_start: 0.7953 (m-40) cc_final: 0.7649 (m-40) REVERT: B 440 LYS cc_start: 0.9047 (mmtp) cc_final: 0.8719 (mtpm) REVERT: B 458 LYS cc_start: 0.7556 (pttt) cc_final: 0.7281 (ptpp) outliers start: 15 outliers final: 4 residues processed: 87 average time/residue: 1.9876 time to fit residues: 182.5405 Evaluate side-chains 79 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 2.348 ------------------------------------------------------------------------------- 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 347 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 549 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 5 optimal weight: 0.9980 chunk 67 optimal weight: 0.0050 chunk 6 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 59 optimal weight: 0.1980 chunk 58 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 ASN B 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.177825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.123743 restraints weight = 7715.920| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.41 r_work: 0.3278 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6639 Z= 0.103 Angle : 0.516 10.609 9028 Z= 0.263 Chirality : 0.040 0.137 941 Planarity : 0.004 0.040 1168 Dihedral : 3.832 25.646 927 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.97 % Favored : 94.52 % Rotamer: Outliers : 2.77 % Allowed : 11.52 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.31), residues: 785 helix: 0.53 (0.29), residues: 361 sheet: 0.47 (0.85), residues: 43 loop : -1.16 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 477 HIS 0.006 0.001 HIS A 241 PHE 0.010 0.001 PHE A 369 TYR 0.016 0.001 TYR A 255 ARG 0.008 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 2) link_NAG-ASN : angle 2.28260 ( 6) link_BETA1-4 : bond 0.00442 ( 1) link_BETA1-4 : angle 1.13284 ( 3) hydrogen bonds : bond 0.03641 ( 252) hydrogen bonds : angle 4.52447 ( 705) SS BOND : bond 0.00638 ( 7) SS BOND : angle 0.91195 ( 14) covalent geometry : bond 0.00220 ( 6629) covalent geometry : angle 0.51209 ( 9005) *********************** 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 94 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7546 (tt0) cc_final: 0.7139 (tm-30) REVERT: A 89 GLN cc_start: 0.6540 (OUTLIER) cc_final: 0.5697 (mt0) REVERT: A 102 GLN cc_start: 0.7999 (mm-40) cc_final: 0.7664 (mm-40) REVERT: A 210 GLU cc_start: 0.8110 (tp30) cc_final: 0.7889 (tp30) REVERT: A 298 MET cc_start: 0.8424 (mtt) cc_final: 0.8202 (mtp) REVERT: A 607 ASN cc_start: 0.4994 (t0) cc_final: 0.4592 (t0) REVERT: B 357 ARG cc_start: 0.8649 (ttp80) cc_final: 0.8217 (ttt90) REVERT: B 405 ASN cc_start: 0.7940 (m-40) cc_final: 0.7620 (m-40) REVERT: B 440 LYS cc_start: 0.9015 (mmtp) cc_final: 0.8699 (mtpm) REVERT: B 458 LYS cc_start: 0.7403 (pttt) cc_final: 0.7125 (ptpp) REVERT: B 471 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7406 (mt-10) outliers start: 19 outliers final: 7 residues processed: 88 average time/residue: 2.1075 time to fit residues: 196.9819 Evaluate side-chains 83 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 59 optimal weight: 0.1980 chunk 17 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.172893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.118510 restraints weight = 7681.427| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.37 r_work: 0.3208 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6639 Z= 0.179 Angle : 0.603 10.277 9028 Z= 0.306 Chirality : 0.043 0.181 941 Planarity : 0.004 0.037 1168 Dihedral : 4.164 25.659 927 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.35 % Favored : 94.14 % Rotamer: Outliers : 3.21 % Allowed : 12.24 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.30), residues: 785 helix: 0.47 (0.29), residues: 358 sheet: 1.16 (0.83), residues: 41 loop : -1.25 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.006 0.002 HIS A 265 PHE 0.013 0.002 PHE A 369 TYR 0.021 0.002 TYR A 385 ARG 0.004 0.001 ARG A 518 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 2) link_NAG-ASN : angle 2.71712 ( 6) link_BETA1-4 : bond 0.00511 ( 1) link_BETA1-4 : angle 1.40156 ( 3) hydrogen bonds : bond 0.04909 ( 252) hydrogen bonds : angle 4.63992 ( 705) SS BOND : bond 0.00743 ( 7) SS BOND : angle 1.30402 ( 14) covalent geometry : bond 0.00428 ( 6629) covalent geometry : angle 0.59687 ( 9005) *********************** 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 92 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7582 (tt0) cc_final: 0.7167 (tm-30) REVERT: A 89 GLN cc_start: 0.6481 (OUTLIER) cc_final: 0.5558 (mt0) REVERT: A 102 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7602 (mm-40) REVERT: A 210 GLU cc_start: 0.8118 (tp30) cc_final: 0.7793 (pt0) REVERT: A 298 MET cc_start: 0.8311 (mtt) cc_final: 0.8033 (mtp) REVERT: A 503 LEU cc_start: 0.6826 (tp) cc_final: 0.6591 (tp) REVERT: A 607 ASN cc_start: 0.5076 (t0) cc_final: 0.4688 (t0) REVERT: B 346 ARG cc_start: 0.7931 (mmt180) cc_final: 0.7340 (ptm160) REVERT: B 357 ARG cc_start: 0.8718 (ttp80) cc_final: 0.8423 (ttp80) REVERT: B 405 ASN cc_start: 0.8077 (m-40) cc_final: 0.7806 (m-40) REVERT: B 458 LYS cc_start: 0.7646 (pttt) cc_final: 0.7348 (ptpp) outliers start: 22 outliers final: 10 residues processed: 85 average time/residue: 1.3366 time to fit residues: 120.1004 Evaluate side-chains 79 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 89 GLN 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 382 VAL 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 1 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.175927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.122260 restraints weight = 7584.471| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.33 r_work: 0.3251 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6639 Z= 0.116 Angle : 0.549 10.671 9028 Z= 0.276 Chirality : 0.041 0.180 941 Planarity : 0.004 0.036 1168 Dihedral : 3.987 25.451 927 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.97 % Favored : 94.52 % Rotamer: Outliers : 2.92 % Allowed : 12.39 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.30), residues: 785 helix: 0.69 (0.29), residues: 354 sheet: 0.60 (0.84), residues: 43 loop : -1.20 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 477 HIS 0.006 0.001 HIS A 241 PHE 0.010 0.001 PHE A 369 TYR 0.014 0.001 TYR A 255 ARG 0.006 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 2) link_NAG-ASN : angle 2.59733 ( 6) link_BETA1-4 : bond 0.00561 ( 1) link_BETA1-4 : angle 1.24044 ( 3) hydrogen bonds : bond 0.03923 ( 252) hydrogen bonds : angle 4.48155 ( 705) SS BOND : bond 0.00841 ( 7) SS BOND : angle 1.79405 ( 14) covalent geometry : bond 0.00258 ( 6629) covalent geometry : angle 0.54079 ( 9005) *********************** 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 91 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 2.318 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7566 (tt0) cc_final: 0.7168 (tm-30) REVERT: A 89 GLN cc_start: 0.6374 (OUTLIER) cc_final: 0.5552 (mt0) REVERT: A 102 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7614 (mm-40) REVERT: A 210 GLU cc_start: 0.8107 (tp30) cc_final: 0.7743 (pt0) REVERT: A 298 MET cc_start: 0.8314 (mtt) cc_final: 0.8056 (mtp) REVERT: A 503 LEU cc_start: 0.6813 (tp) cc_final: 0.6582 (tp) REVERT: A 607 ASN cc_start: 0.4999 (t0) cc_final: 0.4619 (t0) REVERT: B 346 ARG cc_start: 0.7964 (mmt180) cc_final: 0.7323 (ptm160) REVERT: B 357 ARG cc_start: 0.8713 (ttp80) cc_final: 0.8321 (ttp80) REVERT: B 405 ASN cc_start: 0.8053 (m-40) cc_final: 0.7712 (m-40) REVERT: B 458 LYS cc_start: 0.7462 (pttt) cc_final: 0.7170 (ptpp) REVERT: B 471 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7460 (mt-10) outliers start: 20 outliers final: 10 residues processed: 85 average time/residue: 1.7714 time to fit residues: 161.3097 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 : 1.207 ------------------------------------------------------------------------------- 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 318 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 439 LEU 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 50 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 74 optimal weight: 0.0980 chunk 11 optimal weight: 0.0270 chunk 24 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.5440 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.176542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.122556 restraints weight = 7561.583| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.40 r_work: 0.3255 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2528 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= 0.107 Angle : 0.542 10.662 9028 Z= 0.271 Chirality : 0.041 0.199 941 Planarity : 0.004 0.036 1168 Dihedral : 3.917 25.077 927 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.22 % Favored : 94.39 % Rotamer: Outliers : 2.92 % Allowed : 12.68 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.31), residues: 785 helix: 0.88 (0.29), residues: 351 sheet: 0.67 (0.85), residues: 43 loop : -1.16 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 477 HIS 0.006 0.001 HIS A 241 PHE 0.010 0.001 PHE A 369 TYR 0.014 0.001 TYR A 255 ARG 0.002 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00278 ( 2) link_NAG-ASN : angle 2.51803 ( 6) link_BETA1-4 : bond 0.00505 ( 1) link_BETA1-4 : angle 1.19295 ( 3) hydrogen bonds : bond 0.03690 ( 252) hydrogen bonds : angle 4.45459 ( 705) SS BOND : bond 0.00600 ( 7) SS BOND : angle 1.80509 ( 14) covalent geometry : bond 0.00233 ( 6629) covalent geometry : angle 0.53374 ( 9005) *********************** 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 : 0.946 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7586 (tt0) cc_final: 0.7194 (tm-30) REVERT: A 89 GLN cc_start: 0.6383 (OUTLIER) cc_final: 0.5604 (mt0) REVERT: A 102 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7700 (mm-40) REVERT: A 210 GLU cc_start: 0.8076 (tp30) cc_final: 0.7839 (pt0) REVERT: A 246 ARG cc_start: 0.7478 (ttp80) cc_final: 0.6757 (ttp80) REVERT: A 298 MET cc_start: 0.8354 (mtt) cc_final: 0.8102 (mtp) REVERT: A 503 LEU cc_start: 0.6933 (tp) cc_final: 0.6712 (tp) REVERT: A 607 ASN cc_start: 0.5019 (t0) cc_final: 0.4619 (t0) REVERT: B 346 ARG cc_start: 0.8019 (mmt180) cc_final: 0.7356 (ptm160) REVERT: B 357 ARG cc_start: 0.8674 (ttp80) cc_final: 0.8395 (ttp80) REVERT: B 405 ASN cc_start: 0.8045 (m-40) cc_final: 0.7714 (m-40) REVERT: B 458 LYS cc_start: 0.7363 (pttt) cc_final: 0.7079 (ptpp) REVERT: B 471 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7501 (mt-10) outliers start: 20 outliers final: 9 residues processed: 86 average time/residue: 2.0979 time to fit residues: 189.9262 Evaluate side-chains 78 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 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 51 optimal weight: 0.3980 chunk 70 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 30 optimal weight: 0.0020 chunk 58 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.176869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.122929 restraints weight = 7579.676| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.41 r_work: 0.3259 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6639 Z= 0.106 Angle : 0.533 10.650 9028 Z= 0.266 Chirality : 0.041 0.177 941 Planarity : 0.004 0.036 1168 Dihedral : 3.846 25.103 927 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.22 % Favored : 94.39 % Rotamer: Outliers : 2.33 % Allowed : 13.70 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.31), residues: 785 helix: 0.93 (0.29), residues: 351 sheet: 0.65 (0.85), residues: 43 loop : -1.08 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.007 0.001 HIS A 241 PHE 0.010 0.001 PHE A 369 TYR 0.013 0.001 TYR A 255 ARG 0.002 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 2) link_NAG-ASN : angle 2.48495 ( 6) link_BETA1-4 : bond 0.00557 ( 1) link_BETA1-4 : angle 1.19497 ( 3) hydrogen bonds : bond 0.03627 ( 252) hydrogen bonds : angle 4.43783 ( 705) SS BOND : bond 0.00610 ( 7) SS BOND : angle 1.29041 ( 14) covalent geometry : bond 0.00233 ( 6629) covalent geometry : angle 0.52720 ( 9005) *********************** 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 87 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7589 (tt0) cc_final: 0.7196 (tm-30) REVERT: A 89 GLN cc_start: 0.6328 (OUTLIER) cc_final: 0.5619 (mt0) REVERT: A 102 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7689 (mm-40) REVERT: A 210 GLU cc_start: 0.8083 (tp30) cc_final: 0.7841 (pt0) REVERT: A 246 ARG cc_start: 0.7474 (ttp80) cc_final: 0.6739 (ttp80) REVERT: A 255 TYR cc_start: 0.6524 (OUTLIER) cc_final: 0.4435 (t80) REVERT: A 298 MET cc_start: 0.8376 (mtt) cc_final: 0.8143 (mtp) REVERT: A 607 ASN cc_start: 0.5067 (t0) cc_final: 0.4662 (t0) REVERT: B 346 ARG cc_start: 0.8032 (mmt180) cc_final: 0.7366 (ptm160) REVERT: B 357 ARG cc_start: 0.8653 (ttp80) cc_final: 0.8375 (ttp80) REVERT: B 405 ASN cc_start: 0.8008 (m-40) cc_final: 0.7683 (m-40) REVERT: B 458 LYS cc_start: 0.7328 (pttt) cc_final: 0.7050 (ptpp) REVERT: B 471 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7483 (mt-10) outliers start: 16 outliers final: 9 residues processed: 85 average time/residue: 1.0607 time to fit residues: 95.5496 Evaluate side-chains 81 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 216 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 54 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 0.1980 chunk 29 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3990 r_free = 0.3990 target = 0.176728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.122562 restraints weight = 7702.011| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.43 r_work: 0.3252 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6639 Z= 0.113 Angle : 0.542 10.626 9028 Z= 0.270 Chirality : 0.041 0.170 941 Planarity : 0.004 0.035 1168 Dihedral : 3.846 25.038 927 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.10 % Favored : 94.39 % Rotamer: Outliers : 2.33 % Allowed : 13.70 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.31), residues: 785 helix: 0.97 (0.29), residues: 351 sheet: 0.75 (0.86), residues: 43 loop : -1.07 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.008 0.001 HIS A 241 PHE 0.010 0.001 PHE A 369 TYR 0.020 0.001 TYR A 243 ARG 0.002 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 2) link_NAG-ASN : angle 2.50435 ( 6) link_BETA1-4 : bond 0.00551 ( 1) link_BETA1-4 : angle 1.18806 ( 3) hydrogen bonds : bond 0.03719 ( 252) hydrogen bonds : angle 4.41493 ( 705) SS BOND : bond 0.00634 ( 7) SS BOND : angle 1.07509 ( 14) covalent geometry : bond 0.00253 ( 6629) covalent geometry : angle 0.53716 ( 9005) *********************** 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 84 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7586 (tt0) cc_final: 0.7179 (tm-30) REVERT: A 89 GLN cc_start: 0.6322 (OUTLIER) cc_final: 0.5653 (mt0) REVERT: A 102 GLN cc_start: 0.7933 (mm-40) cc_final: 0.7689 (mm-40) REVERT: A 210 GLU cc_start: 0.8057 (tp30) cc_final: 0.7805 (pt0) REVERT: A 246 ARG cc_start: 0.7434 (ttp80) cc_final: 0.6726 (ttp80) REVERT: A 255 TYR cc_start: 0.6560 (OUTLIER) cc_final: 0.4483 (t80) REVERT: A 298 MET cc_start: 0.8331 (mtt) cc_final: 0.8095 (mtp) REVERT: A 607 ASN cc_start: 0.5025 (t0) cc_final: 0.4654 (t0) REVERT: B 346 ARG cc_start: 0.8020 (mmt180) cc_final: 0.7353 (ptm160) REVERT: B 357 ARG cc_start: 0.8638 (ttp80) cc_final: 0.8358 (ttp80) REVERT: B 405 ASN cc_start: 0.8023 (m-40) cc_final: 0.7699 (m-40) REVERT: B 458 LYS cc_start: 0.7323 (pttt) cc_final: 0.6952 (ptpt) REVERT: B 471 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7457 (mt-10) outliers start: 16 outliers final: 9 residues processed: 82 average time/residue: 1.2208 time to fit residues: 105.4329 Evaluate side-chains 78 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 216 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 45 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 58 optimal weight: 0.0170 chunk 72 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.2026 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.173129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.131316 restraints weight = 7664.899| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.79 r_work: 0.3187 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 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 : 0.004 0.033 6639 Z= 0.169 Angle : 0.606 10.415 9028 Z= 0.304 Chirality : 0.043 0.202 941 Planarity : 0.004 0.035 1168 Dihedral : 4.122 25.218 927 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.86 % Favored : 93.89 % Rotamer: Outliers : 2.04 % Allowed : 14.43 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.31), residues: 785 helix: 0.80 (0.29), residues: 353 sheet: 0.88 (0.85), residues: 43 loop : -1.10 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 477 HIS 0.009 0.002 HIS A 241 PHE 0.012 0.002 PHE A 369 TYR 0.019 0.002 TYR A 243 ARG 0.003 0.000 ARG A 518 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 2) link_NAG-ASN : angle 2.83965 ( 6) link_BETA1-4 : bond 0.00528 ( 1) link_BETA1-4 : angle 1.29142 ( 3) hydrogen bonds : bond 0.04609 ( 252) hydrogen bonds : angle 4.53180 ( 705) SS BOND : bond 0.00806 ( 7) SS BOND : angle 1.27845 ( 14) covalent geometry : bond 0.00401 ( 6629) covalent geometry : angle 0.59986 ( 9005) ********************** 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 82 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7625 (tt0) cc_final: 0.7294 (tm-30) REVERT: A 89 GLN cc_start: 0.6700 (OUTLIER) cc_final: 0.5875 (mt0) REVERT: A 102 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7679 (mm-40) REVERT: A 255 TYR cc_start: 0.6609 (OUTLIER) cc_final: 0.4531 (t80) REVERT: A 298 MET cc_start: 0.8456 (mtt) cc_final: 0.8213 (mtp) REVERT: A 503 LEU cc_start: 0.7141 (tp) cc_final: 0.6895 (tp) REVERT: A 607 ASN cc_start: 0.5331 (t0) cc_final: 0.4939 (t0) REVERT: B 346 ARG cc_start: 0.7854 (mmt180) cc_final: 0.7461 (ptm160) REVERT: B 357 ARG cc_start: 0.8594 (ttp80) cc_final: 0.8285 (ttp80) REVERT: B 405 ASN cc_start: 0.8027 (m-40) cc_final: 0.7816 (m-40) REVERT: B 458 LYS cc_start: 0.7376 (pttt) cc_final: 0.7156 (ptpt) REVERT: B 471 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7340 (mt-10) outliers start: 14 outliers final: 9 residues processed: 80 average time/residue: 1.2531 time to fit residues: 106.1867 Evaluate side-chains 77 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 216 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 0.0870 chunk 12 optimal weight: 0.0060 chunk 6 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 59 optimal weight: 0.0970 chunk 23 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 overall best weight: 0.2572 ------------------------------------------------------------------------------- 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 = 0.4013 r_free = 0.4013 target = 0.178397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.136656 restraints weight = 7822.451| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.88 r_work: 0.3238 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6639 Z= 0.092 Angle : 0.524 10.913 9028 Z= 0.261 Chirality : 0.040 0.147 941 Planarity : 0.003 0.034 1168 Dihedral : 3.804 24.478 927 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.22 % Favored : 94.52 % Rotamer: Outliers : 1.60 % Allowed : 15.01 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.31), residues: 785 helix: 1.04 (0.29), residues: 352 sheet: 0.86 (0.86), residues: 43 loop : -1.00 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 477 HIS 0.010 0.001 HIS A 241 PHE 0.009 0.001 PHE A 327 TYR 0.018 0.001 TYR A 243 ARG 0.002 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 2) link_NAG-ASN : angle 2.52015 ( 6) link_BETA1-4 : bond 0.00595 ( 1) link_BETA1-4 : angle 1.04667 ( 3) hydrogen bonds : bond 0.03208 ( 252) hydrogen bonds : angle 4.34784 ( 705) SS BOND : bond 0.00516 ( 7) SS BOND : angle 0.91607 ( 14) covalent geometry : bond 0.00189 ( 6629) covalent geometry : angle 0.51875 ( 9005) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6223.48 seconds wall clock time: 112 minutes 49.80 seconds (6769.80 seconds total)