Starting phenix.real_space_refine on Sun Apr 27 18:53:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wox_37701/04_2025/8wox_37701.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wox_37701/04_2025/8wox_37701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wox_37701/04_2025/8wox_37701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wox_37701/04_2025/8wox_37701.map" model { file = "/net/cci-nas-00/data/ceres_data/8wox_37701/04_2025/8wox_37701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wox_37701/04_2025/8wox_37701.cif" } resolution = 2.75 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 36 5.16 5 C 4060 2.51 5 N 1050 2.21 5 O 1201 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6348 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1537 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "A" Number of atoms: 4796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4796 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 25, 'TRANS': 562} Chain breaks: 1 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 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.71, per 1000 atoms: 0.90 Number of scatterers: 6348 At special positions: 0 Unit cell: (93.28, 77.44, 124.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 36 16.00 O 1201 8.00 N 1050 7.00 C 4060 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 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=2.03 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 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=2.03 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 NAG-ASN " NAG B 601 " - " ASN B 343 " Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 840.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1470 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 56.1% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.570A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.644A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.519A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 389' Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.539A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 417 through 422' Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.614A pdb=" N GLN A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 80 removed outlier: 3.674A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 103 removed outlier: 3.732A pdb=" N SER A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.548A pdb=" N ILE A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 155 removed outlier: 4.336A pdb=" N ASP A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.861A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 208 Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.541A pdb=" N TYR A 215 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP A 216 " --> pdb=" O ASP A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 216' Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.898A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.767A pdb=" N GLN A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASP A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.639A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 303 through 317 removed outlier: 3.613A pdb=" N ILE A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 317 " --> pdb=" O LYS A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 4.062A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.633A pdb=" N PHE A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.935A 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 399 through 413 removed outlier: 3.565A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.501A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.611A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (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 512 through 533 removed outlier: 4.523A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.671A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.566A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.643A pdb=" N GLU A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A 598 " --> pdb=" O TRP A 594 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.614A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.726A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.302A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.075A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) 279 hydrogen bonds defined for protein. 792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2036 1.34 - 1.46: 1680 1.46 - 1.58: 2749 1.58 - 1.70: 0 1.70 - 1.82: 57 Bond restraints: 6522 Sorted by residual: bond pdb=" C ASP A 499 " pdb=" N PRO A 500 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.28e-02 6.10e+03 1.57e+00 bond pdb=" C3 NAG B 601 " pdb=" O3 NAG B 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.84e-01 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.425 -0.019 2.00e-02 2.50e+03 9.12e-01 bond pdb=" C GLU A 35 " pdb=" O GLU A 35 " ideal model delta sigma weight residual 1.237 1.248 -0.011 1.19e-02 7.06e+03 8.59e-01 bond pdb=" C5 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.413 1.431 -0.018 2.00e-02 2.50e+03 8.10e-01 ... (remaining 6517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 8554 1.23 - 2.46: 240 2.46 - 3.69: 38 3.69 - 4.92: 21 4.92 - 6.15: 3 Bond angle restraints: 8856 Sorted by residual: angle pdb=" CA ILE A 513 " pdb=" C ILE A 513 " pdb=" N ARG A 514 " ideal model delta sigma weight residual 118.48 115.70 2.78 1.01e+00 9.80e-01 7.58e+00 angle pdb=" CA CYS B 525 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " ideal model delta sigma weight residual 114.40 120.55 -6.15 2.30e+00 1.89e-01 7.16e+00 angle pdb=" N ILE A 513 " pdb=" CA ILE A 513 " pdb=" C ILE A 513 " ideal model delta sigma weight residual 113.07 109.44 3.63 1.37e+00 5.33e-01 7.01e+00 angle pdb=" CA CYS B 391 " pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " ideal model delta sigma weight residual 114.40 119.83 -5.43 2.30e+00 1.89e-01 5.57e+00 angle pdb=" C TRP A 459 " pdb=" N ARG A 460 " pdb=" CA ARG A 460 " ideal model delta sigma weight residual 120.29 117.04 3.25 1.42e+00 4.96e-01 5.23e+00 ... (remaining 8851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.13: 3626 22.13 - 44.26: 204 44.26 - 66.39: 21 66.39 - 88.53: 10 88.53 - 110.66: 4 Dihedral angle restraints: 3865 sinusoidal: 1573 harmonic: 2292 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual -86.00 -5.68 -80.32 1 1.00e+01 1.00e-02 7.99e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 34.94 58.06 1 1.00e+01 1.00e-02 4.52e+01 dihedral pdb=" CA VAL B 524 " pdb=" C VAL B 524 " pdb=" N CYS B 525 " pdb=" CA CYS B 525 " ideal model delta harmonic sigma weight residual 180.00 160.41 19.59 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 3862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 479 0.027 - 0.054: 294 0.054 - 0.080: 96 0.080 - 0.107: 44 0.107 - 0.134: 16 Chirality restraints: 929 Sorted by residual: chirality pdb=" CA ILE A 468 " pdb=" N ILE A 468 " pdb=" C ILE A 468 " pdb=" CB ILE A 468 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 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 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA CYS B 525 " pdb=" N CYS B 525 " pdb=" C CYS B 525 " pdb=" CB CYS B 525 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 926 not shown) Planarity restraints: 1145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 468 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.99e+00 pdb=" N PRO A 469 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 469 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 469 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 414 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO A 415 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 611 " -0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO A 612 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 612 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 612 " -0.021 5.00e-02 4.00e+02 ... (remaining 1142 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 64 2.66 - 3.22: 5695 3.22 - 3.78: 9181 3.78 - 4.34: 12136 4.34 - 4.90: 20582 Nonbonded interactions: 47658 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.099 2.230 nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.100 2.230 nonbonded pdb=" OG SER A 563 " pdb=" OE1 GLU A 564 " model vdw 2.176 3.040 nonbonded pdb=" OG SER A 331 " pdb=" O ILE A 358 " model vdw 2.247 3.040 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.250 3.120 ... (remaining 47653 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.350 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.830 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: 0.010 Load rotamer database and sin/cos tables:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.205 6531 Z= 0.188 Angle : 0.540 6.624 8871 Z= 0.295 Chirality : 0.041 0.134 929 Planarity : 0.004 0.056 1144 Dihedral : 13.941 110.656 2377 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: 0.02 (0.31), residues: 776 helix: 0.85 (0.29), residues: 366 sheet: 2.45 (0.76), residues: 44 loop : -1.18 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS A 401 PHE 0.016 0.001 PHE A 400 TYR 0.013 0.001 TYR A 587 ARG 0.002 0.000 ARG A 514 Details of bonding type rmsd link_NAG-ASN : bond 0.00177 ( 1) link_NAG-ASN : angle 2.84613 ( 3) hydrogen bonds : bond 0.18168 ( 279) hydrogen bonds : angle 5.66185 ( 792) metal coordination : bond 0.20276 ( 2) SS BOND : bond 0.00138 ( 6) SS BOND : angle 2.52784 ( 12) covalent geometry : bond 0.00314 ( 6522) covalent geometry : angle 0.52989 ( 8856) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.617 Fit side-chains REVERT: A 74 GLU cc_start: 0.7578 (tp30) cc_final: 0.7172 (tp30) REVERT: A 75 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7388 (tm-30) REVERT: A 126 ILE cc_start: 0.8350 (tt) cc_final: 0.8005 (tt) REVERT: A 224 ASP cc_start: 0.7668 (m-30) cc_final: 0.7395 (m-30) REVERT: A 334 THR cc_start: 0.8472 (t) cc_final: 0.8247 (m) REVERT: A 335 GLU cc_start: 0.7697 (tp30) cc_final: 0.7047 (mm-30) REVERT: A 338 ASP cc_start: 0.7256 (p0) cc_final: 0.6853 (p0) REVERT: A 341 LYS cc_start: 0.7911 (mttt) cc_final: 0.7709 (mttt) REVERT: A 376 MET cc_start: 0.8691 (tpp) cc_final: 0.8388 (mmt) REVERT: A 470 LYS cc_start: 0.8152 (tppp) cc_final: 0.7880 (tppp) REVERT: A 509 ASP cc_start: 0.7027 (p0) cc_final: 0.6639 (p0) REVERT: A 597 GLU cc_start: 0.7990 (tp30) cc_final: 0.7753 (mm-30) outliers start: 0 outliers final: 1 residues processed: 199 average time/residue: 1.1130 time to fit residues: 232.5804 Evaluate side-chains 169 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 0.0970 chunk 19 optimal weight: 0.0980 chunk 39 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN B 481 ASN A 42 GLN A 401 HIS A 524 GLN A 598 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.120550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.109439 restraints weight = 9548.022| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.90 r_work: 0.3462 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6531 Z= 0.192 Angle : 0.604 7.036 8871 Z= 0.311 Chirality : 0.044 0.181 929 Planarity : 0.005 0.046 1144 Dihedral : 7.976 68.216 877 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.64 % Allowed : 15.12 % Favored : 82.23 % 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: 0.19 (0.31), residues: 776 helix: 1.04 (0.28), residues: 376 sheet: 2.22 (0.76), residues: 49 loop : -1.23 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 353 HIS 0.007 0.001 HIS A 241 PHE 0.027 0.002 PHE A 504 TYR 0.024 0.002 TYR A 183 ARG 0.006 0.000 ARG A 340 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 1) link_NAG-ASN : angle 2.39380 ( 3) hydrogen bonds : bond 0.06997 ( 279) hydrogen bonds : angle 4.27086 ( 792) metal coordination : bond 0.00868 ( 2) SS BOND : bond 0.00224 ( 6) SS BOND : angle 2.23797 ( 12) covalent geometry : bond 0.00440 ( 6522) covalent geometry : angle 0.59735 ( 8856) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 408 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8193 (ptm-80) REVERT: A 30 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: A 74 GLU cc_start: 0.7944 (tp30) cc_final: 0.7546 (tp30) REVERT: A 75 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7640 (tm-30) REVERT: A 160 GLU cc_start: 0.8064 (tp30) cc_final: 0.7859 (tt0) REVERT: A 334 THR cc_start: 0.8593 (t) cc_final: 0.8333 (m) REVERT: A 335 GLU cc_start: 0.7992 (tp30) cc_final: 0.7164 (mm-30) REVERT: A 455 MET cc_start: 0.8078 (tmm) cc_final: 0.7850 (tmm) REVERT: A 470 LYS cc_start: 0.8398 (tppp) cc_final: 0.8177 (tppp) REVERT: A 509 ASP cc_start: 0.7133 (p0) cc_final: 0.6803 (p0) REVERT: A 564 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7529 (mp0) outliers start: 18 outliers final: 4 residues processed: 177 average time/residue: 1.1068 time to fit residues: 205.8582 Evaluate side-chains 169 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 162 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 564 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 chunk 47 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 0.0870 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 17 optimal weight: 0.4980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN B 388 ASN A 101 GLN A 572 ASN A 598 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.120433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.108900 restraints weight = 9586.695| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.91 r_work: 0.3456 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6531 Z= 0.188 Angle : 0.575 8.245 8871 Z= 0.298 Chirality : 0.043 0.151 929 Planarity : 0.004 0.043 1144 Dihedral : 6.397 55.001 875 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.64 % Allowed : 17.91 % Favored : 79.44 % 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: 0.15 (0.30), residues: 776 helix: 1.04 (0.28), residues: 378 sheet: 2.06 (0.76), residues: 49 loop : -1.28 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 353 HIS 0.005 0.001 HIS A 241 PHE 0.020 0.002 PHE A 504 TYR 0.023 0.002 TYR A 183 ARG 0.006 0.000 ARG A 340 Details of bonding type rmsd link_NAG-ASN : bond 0.00659 ( 1) link_NAG-ASN : angle 2.75995 ( 3) hydrogen bonds : bond 0.06718 ( 279) hydrogen bonds : angle 4.17955 ( 792) metal coordination : bond 0.00396 ( 2) SS BOND : bond 0.00211 ( 6) SS BOND : angle 2.17383 ( 12) covalent geometry : bond 0.00434 ( 6522) covalent geometry : angle 0.56768 ( 8856) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: B 524 VAL cc_start: 0.7350 (OUTLIER) cc_final: 0.7114 (p) REVERT: A 30 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: A 74 GLU cc_start: 0.7956 (tp30) cc_final: 0.7699 (tp30) REVERT: A 75 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7646 (tm-30) REVERT: A 160 GLU cc_start: 0.8085 (tp30) cc_final: 0.7873 (tt0) REVERT: A 190 MET cc_start: 0.8114 (ttp) cc_final: 0.7781 (ttt) REVERT: A 334 THR cc_start: 0.8633 (t) cc_final: 0.8389 (m) REVERT: A 335 GLU cc_start: 0.8033 (tp30) cc_final: 0.7238 (mm-30) REVERT: A 341 LYS cc_start: 0.8144 (mttt) cc_final: 0.7847 (mttt) REVERT: A 455 MET cc_start: 0.8058 (tmm) cc_final: 0.7820 (tmm) REVERT: A 470 LYS cc_start: 0.8405 (tppp) cc_final: 0.8199 (tppp) REVERT: A 509 ASP cc_start: 0.7227 (p0) cc_final: 0.6906 (p0) REVERT: A 564 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: A 568 LEU cc_start: 0.8634 (tp) cc_final: 0.8403 (tt) REVERT: A 596 LYS cc_start: 0.8533 (mtmm) cc_final: 0.8299 (mtmm) outliers start: 18 outliers final: 5 residues processed: 174 average time/residue: 1.0676 time to fit residues: 195.7430 Evaluate side-chains 169 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 161 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 611 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 53 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 57 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 chunk 58 optimal weight: 0.0980 chunk 25 optimal weight: 0.3980 chunk 46 optimal weight: 0.9980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN B 388 ASN A 572 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.120589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.109107 restraints weight = 9791.446| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.94 r_work: 0.3454 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6531 Z= 0.170 Angle : 0.576 7.458 8871 Z= 0.291 Chirality : 0.042 0.162 929 Planarity : 0.004 0.044 1144 Dihedral : 5.709 53.434 875 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.35 % Allowed : 19.38 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.31), residues: 776 helix: 1.12 (0.28), residues: 376 sheet: 2.00 (0.75), residues: 49 loop : -1.23 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 349 HIS 0.005 0.001 HIS A 241 PHE 0.019 0.001 PHE A 28 TYR 0.023 0.001 TYR A 183 ARG 0.007 0.000 ARG A 340 Details of bonding type rmsd link_NAG-ASN : bond 0.00619 ( 1) link_NAG-ASN : angle 3.19823 ( 3) hydrogen bonds : bond 0.06343 ( 279) hydrogen bonds : angle 4.11029 ( 792) metal coordination : bond 0.00392 ( 2) SS BOND : bond 0.00189 ( 6) SS BOND : angle 2.11551 ( 12) covalent geometry : bond 0.00390 ( 6522) covalent geometry : angle 0.56775 ( 8856) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: A 74 GLU cc_start: 0.7915 (tp30) cc_final: 0.7472 (tp30) REVERT: A 75 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7636 (tm-30) REVERT: A 334 THR cc_start: 0.8591 (t) cc_final: 0.8371 (m) REVERT: A 335 GLU cc_start: 0.8040 (tp30) cc_final: 0.7300 (mm-30) REVERT: A 455 MET cc_start: 0.8070 (tmm) cc_final: 0.7851 (tmm) REVERT: A 509 ASP cc_start: 0.7118 (p0) cc_final: 0.6806 (p0) REVERT: A 564 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: A 596 LYS cc_start: 0.8527 (mtmm) cc_final: 0.8296 (mtmm) outliers start: 16 outliers final: 7 residues processed: 169 average time/residue: 1.4966 time to fit residues: 267.5754 Evaluate side-chains 172 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 611 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 16 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 44 optimal weight: 0.0470 chunk 23 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN B 388 ASN A 175 GLN A 572 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.118388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.107232 restraints weight = 9585.507| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.90 r_work: 0.3426 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 6531 Z= 0.246 Angle : 0.633 9.597 8871 Z= 0.324 Chirality : 0.045 0.135 929 Planarity : 0.005 0.049 1144 Dihedral : 5.442 55.070 875 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.94 % Allowed : 19.97 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.07 (0.30), residues: 776 helix: 1.11 (0.28), residues: 371 sheet: 1.97 (0.74), residues: 49 loop : -1.43 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 477 HIS 0.007 0.002 HIS A 241 PHE 0.023 0.002 PHE A 28 TYR 0.025 0.002 TYR A 587 ARG 0.006 0.000 ARG A 340 Details of bonding type rmsd link_NAG-ASN : bond 0.00562 ( 1) link_NAG-ASN : angle 3.90158 ( 3) hydrogen bonds : bond 0.07393 ( 279) hydrogen bonds : angle 4.22937 ( 792) metal coordination : bond 0.00615 ( 2) SS BOND : bond 0.00319 ( 6) SS BOND : angle 2.35095 ( 12) covalent geometry : bond 0.00579 ( 6522) covalent geometry : angle 0.62312 ( 8856) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 350 VAL cc_start: 0.8185 (t) cc_final: 0.7946 (p) REVERT: B 408 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8161 (ptm-80) REVERT: A 30 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: A 74 GLU cc_start: 0.7926 (tp30) cc_final: 0.7698 (tp30) REVERT: A 75 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7681 (tm-30) REVERT: A 190 MET cc_start: 0.8172 (tmm) cc_final: 0.7731 (ttt) REVERT: A 335 GLU cc_start: 0.8035 (tp30) cc_final: 0.7489 (mm-30) REVERT: A 455 MET cc_start: 0.8044 (tmm) cc_final: 0.7707 (tmm) REVERT: A 509 ASP cc_start: 0.7266 (p0) cc_final: 0.6961 (p0) REVERT: A 525 PHE cc_start: 0.8506 (m-10) cc_final: 0.8300 (m-10) REVERT: A 564 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7617 (mp0) outliers start: 20 outliers final: 10 residues processed: 175 average time/residue: 1.5753 time to fit residues: 291.8545 Evaluate side-chains 176 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 611 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 58 optimal weight: 0.1980 chunk 68 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 73 optimal weight: 0.3980 chunk 38 optimal weight: 0.3980 chunk 67 optimal weight: 0.9990 chunk 63 optimal weight: 0.0070 overall best weight: 0.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN B 388 ASN A 394 ASN A 572 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.120747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.109537 restraints weight = 9566.783| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.92 r_work: 0.3467 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6531 Z= 0.151 Angle : 0.592 8.453 8871 Z= 0.299 Chirality : 0.041 0.127 929 Planarity : 0.004 0.045 1144 Dihedral : 5.156 58.038 875 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.96 % Allowed : 19.82 % Favored : 76.21 % 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: 0.32 (0.31), residues: 776 helix: 1.31 (0.28), residues: 371 sheet: 1.71 (0.75), residues: 51 loop : -1.25 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 353 HIS 0.004 0.001 HIS A 241 PHE 0.019 0.001 PHE A 28 TYR 0.022 0.001 TYR A 183 ARG 0.008 0.000 ARG A 340 Details of bonding type rmsd link_NAG-ASN : bond 0.00292 ( 1) link_NAG-ASN : angle 4.03829 ( 3) hydrogen bonds : bond 0.05937 ( 279) hydrogen bonds : angle 4.04342 ( 792) metal coordination : bond 0.00293 ( 2) SS BOND : bond 0.00296 ( 6) SS BOND : angle 2.16970 ( 12) covalent geometry : bond 0.00344 ( 6522) covalent geometry : angle 0.58200 ( 8856) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 350 VAL cc_start: 0.8197 (t) cc_final: 0.7926 (p) REVERT: B 408 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8198 (ptm-80) REVERT: A 30 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7211 (mp0) REVERT: A 66 GLU cc_start: 0.7961 (tp30) cc_final: 0.7567 (tp30) REVERT: A 74 GLU cc_start: 0.7890 (tp30) cc_final: 0.7464 (tp30) REVERT: A 75 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7652 (tm-30) REVERT: A 190 MET cc_start: 0.8153 (tmm) cc_final: 0.7691 (ttt) REVERT: A 335 GLU cc_start: 0.8076 (tp30) cc_final: 0.7521 (mm-30) REVERT: A 435 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7218 (mt-10) REVERT: A 509 ASP cc_start: 0.7111 (p0) cc_final: 0.6792 (p0) REVERT: A 564 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7587 (mp0) outliers start: 27 outliers final: 11 residues processed: 176 average time/residue: 1.7934 time to fit residues: 336.2808 Evaluate side-chains 175 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 611 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 0.6980 chunk 52 optimal weight: 0.0980 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN B 388 ASN A 175 GLN A 493 HIS A 572 ASN A 598 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.119747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.108341 restraints weight = 9481.340| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.92 r_work: 0.3445 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6531 Z= 0.204 Angle : 0.630 7.598 8871 Z= 0.321 Chirality : 0.044 0.130 929 Planarity : 0.005 0.045 1144 Dihedral : 5.048 52.374 875 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.11 % Allowed : 19.97 % Favored : 75.92 % 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: 0.23 (0.31), residues: 776 helix: 1.28 (0.28), residues: 370 sheet: 1.74 (0.74), residues: 51 loop : -1.35 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 477 HIS 0.006 0.001 HIS A 241 PHE 0.027 0.002 PHE A 28 TYR 0.023 0.002 TYR A 183 ARG 0.007 0.000 ARG A 340 Details of bonding type rmsd link_NAG-ASN : bond 0.00124 ( 1) link_NAG-ASN : angle 4.51333 ( 3) hydrogen bonds : bond 0.06807 ( 279) hydrogen bonds : angle 4.11821 ( 792) metal coordination : bond 0.00447 ( 2) SS BOND : bond 0.00257 ( 6) SS BOND : angle 2.26315 ( 12) covalent geometry : bond 0.00477 ( 6522) covalent geometry : angle 0.61923 ( 8856) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 350 VAL cc_start: 0.8217 (t) cc_final: 0.7904 (p) REVERT: B 365 TYR cc_start: 0.8554 (m-10) cc_final: 0.8192 (m-10) REVERT: B 408 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8180 (ptm-80) REVERT: B 524 VAL cc_start: 0.7577 (OUTLIER) cc_final: 0.7350 (p) REVERT: A 30 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: A 66 GLU cc_start: 0.7984 (tp30) cc_final: 0.7553 (tp30) REVERT: A 74 GLU cc_start: 0.7968 (tp30) cc_final: 0.7509 (tp30) REVERT: A 75 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7660 (tm-30) REVERT: A 190 MET cc_start: 0.8207 (tmm) cc_final: 0.7742 (ttt) REVERT: A 335 GLU cc_start: 0.7921 (tp30) cc_final: 0.7380 (mm-30) REVERT: A 435 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7266 (mt-10) REVERT: A 509 ASP cc_start: 0.7197 (p0) cc_final: 0.6892 (p0) REVERT: A 564 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: A 596 LYS cc_start: 0.8499 (mtmm) cc_final: 0.8245 (mttm) outliers start: 28 outliers final: 14 residues processed: 170 average time/residue: 1.0811 time to fit residues: 193.6509 Evaluate side-chains 177 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 611 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 64 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 11 optimal weight: 0.0980 chunk 24 optimal weight: 0.9990 chunk 57 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 10 optimal weight: 0.0270 chunk 46 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 51 optimal weight: 0.0980 overall best weight: 0.2038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN B 388 ASN A 572 ASN A 598 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.123303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.111743 restraints weight = 9502.350| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.94 r_work: 0.3495 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6531 Z= 0.123 Angle : 0.584 10.197 8871 Z= 0.292 Chirality : 0.040 0.130 929 Planarity : 0.004 0.045 1144 Dihedral : 4.592 43.877 875 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.50 % Allowed : 22.32 % Favored : 75.18 % 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: 0.46 (0.31), residues: 776 helix: 1.45 (0.28), residues: 368 sheet: 1.76 (0.75), residues: 51 loop : -1.19 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 69 HIS 0.003 0.001 HIS A 241 PHE 0.025 0.001 PHE A 28 TYR 0.022 0.001 TYR A 183 ARG 0.007 0.000 ARG A 340 Details of bonding type rmsd link_NAG-ASN : bond 0.00136 ( 1) link_NAG-ASN : angle 4.19715 ( 3) hydrogen bonds : bond 0.05120 ( 279) hydrogen bonds : angle 3.96787 ( 792) metal coordination : bond 0.00171 ( 2) SS BOND : bond 0.00087 ( 6) SS BOND : angle 1.98928 ( 12) covalent geometry : bond 0.00271 ( 6522) covalent geometry : angle 0.57477 ( 8856) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: B 365 TYR cc_start: 0.8539 (m-10) cc_final: 0.8195 (m-10) REVERT: B 524 VAL cc_start: 0.7534 (OUTLIER) cc_final: 0.7261 (p) REVERT: A 30 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: A 66 GLU cc_start: 0.7924 (tp30) cc_final: 0.7503 (tp30) REVERT: A 74 GLU cc_start: 0.7927 (tp30) cc_final: 0.7504 (tp30) REVERT: A 75 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7738 (tm-30) REVERT: A 190 MET cc_start: 0.8206 (tmm) cc_final: 0.7688 (ttt) REVERT: A 335 GLU cc_start: 0.7939 (tp30) cc_final: 0.7375 (mm-30) REVERT: A 509 ASP cc_start: 0.7080 (p0) cc_final: 0.6756 (p0) REVERT: A 564 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7547 (mp0) outliers start: 17 outliers final: 8 residues processed: 169 average time/residue: 1.1385 time to fit residues: 202.1187 Evaluate side-chains 170 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 564 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 72 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 70 optimal weight: 0.0870 chunk 46 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 33 optimal weight: 0.2980 chunk 47 optimal weight: 0.2980 chunk 49 optimal weight: 0.0170 chunk 38 optimal weight: 0.9980 overall best weight: 0.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN B 388 ASN A 175 GLN A 572 ASN A 598 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.122254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.110760 restraints weight = 9569.607| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.95 r_work: 0.3482 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6531 Z= 0.134 Angle : 0.584 9.623 8871 Z= 0.293 Chirality : 0.041 0.153 929 Planarity : 0.004 0.044 1144 Dihedral : 4.510 44.024 875 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.64 % Allowed : 22.76 % Favored : 74.60 % 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: 0.53 (0.31), residues: 776 helix: 1.54 (0.28), residues: 368 sheet: 1.72 (0.74), residues: 51 loop : -1.17 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 69 HIS 0.004 0.001 HIS A 241 PHE 0.024 0.001 PHE A 28 TYR 0.021 0.001 TYR A 183 ARG 0.008 0.000 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00111 ( 1) link_NAG-ASN : angle 4.21714 ( 3) hydrogen bonds : bond 0.05416 ( 279) hydrogen bonds : angle 3.90772 ( 792) metal coordination : bond 0.00256 ( 2) SS BOND : bond 0.00137 ( 6) SS BOND : angle 2.03955 ( 12) covalent geometry : bond 0.00302 ( 6522) covalent geometry : angle 0.57466 ( 8856) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: B 350 VAL cc_start: 0.8129 (t) cc_final: 0.7823 (p) REVERT: A 30 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: A 66 GLU cc_start: 0.7933 (tp30) cc_final: 0.7519 (tp30) REVERT: A 74 GLU cc_start: 0.7947 (tp30) cc_final: 0.7524 (tp30) REVERT: A 75 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7744 (tm-30) REVERT: A 190 MET cc_start: 0.8186 (tmm) cc_final: 0.7663 (ttt) REVERT: A 333 LEU cc_start: 0.8684 (mm) cc_final: 0.8455 (mt) REVERT: A 335 GLU cc_start: 0.7917 (tp30) cc_final: 0.7344 (mm-30) REVERT: A 509 ASP cc_start: 0.7144 (p0) cc_final: 0.6815 (p0) REVERT: A 564 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7422 (mp0) outliers start: 18 outliers final: 11 residues processed: 166 average time/residue: 1.0476 time to fit residues: 183.3849 Evaluate side-chains 171 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 564 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 64 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 51 optimal weight: 0.0030 chunk 13 optimal weight: 0.0770 chunk 16 optimal weight: 0.0070 chunk 25 optimal weight: 0.0050 overall best weight: 0.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN B 388 ASN A 300 GLN A 572 ASN A 598 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.125537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.113893 restraints weight = 9634.011| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.95 r_work: 0.3524 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6531 Z= 0.112 Angle : 0.580 9.273 8871 Z= 0.286 Chirality : 0.040 0.159 929 Planarity : 0.004 0.045 1144 Dihedral : 4.308 40.127 875 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.91 % Allowed : 23.49 % Favored : 74.60 % 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: 0.63 (0.31), residues: 776 helix: 1.57 (0.28), residues: 372 sheet: 1.90 (0.75), residues: 46 loop : -1.07 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 478 HIS 0.003 0.001 HIS A 374 PHE 0.022 0.001 PHE A 28 TYR 0.021 0.001 TYR A 183 ARG 0.008 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00141 ( 1) link_NAG-ASN : angle 3.85124 ( 3) hydrogen bonds : bond 0.04437 ( 279) hydrogen bonds : angle 3.82951 ( 792) metal coordination : bond 0.00091 ( 2) SS BOND : bond 0.00266 ( 6) SS BOND : angle 1.83806 ( 12) covalent geometry : bond 0.00243 ( 6522) covalent geometry : angle 0.57173 ( 8856) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: B 365 TYR cc_start: 0.8450 (m-10) cc_final: 0.8099 (m-10) REVERT: B 376 THR cc_start: 0.8455 (OUTLIER) cc_final: 0.8189 (p) REVERT: B 524 VAL cc_start: 0.7437 (OUTLIER) cc_final: 0.7148 (p) REVERT: A 30 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6977 (mp0) REVERT: A 66 GLU cc_start: 0.7913 (tp30) cc_final: 0.7494 (tp30) REVERT: A 74 GLU cc_start: 0.7915 (tp30) cc_final: 0.7513 (tp30) REVERT: A 75 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7744 (tm-30) REVERT: A 190 MET cc_start: 0.8136 (tmm) cc_final: 0.7587 (ttt) REVERT: A 333 LEU cc_start: 0.8686 (mm) cc_final: 0.8458 (mt) REVERT: A 335 GLU cc_start: 0.7960 (tp30) cc_final: 0.7428 (mm-30) REVERT: A 509 ASP cc_start: 0.7046 (p0) cc_final: 0.6717 (p0) REVERT: A 564 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7433 (mp0) outliers start: 13 outliers final: 8 residues processed: 165 average time/residue: 1.0700 time to fit residues: 185.9720 Evaluate side-chains 171 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 564 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 36 optimal weight: 0.9990 chunk 34 optimal weight: 0.2980 chunk 20 optimal weight: 0.3980 chunk 76 optimal weight: 0.4980 chunk 33 optimal weight: 0.0980 chunk 29 optimal weight: 0.4980 chunk 51 optimal weight: 0.2980 chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN B 388 ASN A 572 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.122366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.110774 restraints weight = 9761.493| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.98 r_work: 0.3482 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6531 Z= 0.151 Angle : 0.611 9.461 8871 Z= 0.306 Chirality : 0.042 0.152 929 Planarity : 0.004 0.043 1144 Dihedral : 4.488 43.555 875 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.35 % Allowed : 23.94 % Favored : 73.72 % 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: 0.59 (0.31), residues: 776 helix: 1.57 (0.28), residues: 371 sheet: 1.74 (0.74), residues: 51 loop : -1.14 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 69 HIS 0.004 0.001 HIS A 241 PHE 0.024 0.001 PHE A 28 TYR 0.022 0.001 TYR A 183 ARG 0.010 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00067 ( 1) link_NAG-ASN : angle 4.28931 ( 3) hydrogen bonds : bond 0.05653 ( 279) hydrogen bonds : angle 3.88371 ( 792) metal coordination : bond 0.00320 ( 2) SS BOND : bond 0.00146 ( 6) SS BOND : angle 2.07388 ( 12) covalent geometry : bond 0.00348 ( 6522) covalent geometry : angle 0.60131 ( 8856) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6363.17 seconds wall clock time: 111 minutes 42.43 seconds (6702.43 seconds total)