Starting phenix.real_space_refine on Fri Aug 22 17:22:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wox_37701/08_2025/8wox_37701.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wox_37701/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8wox_37701/08_2025/8wox_37701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wox_37701/08_2025/8wox_37701.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wox_37701/08_2025/8wox_37701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wox_37701/08_2025/8wox_37701.map" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.69, per 1000 atoms: 0.27 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: 0.55 Conformation dependent library (CDL) restraints added in 408.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.17 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: 0.81 Time building geometry restraints manager: 0.70 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: 10.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.190 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.570 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.31), residues: 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 ARG 0.002 0.000 ARG A 514 TYR 0.013 0.001 TYR A 587 PHE 0.016 0.001 PHE A 400 TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6522) covalent geometry : angle 0.52989 ( 8856) SS BOND : bond 0.00138 ( 6) SS BOND : angle 2.52784 ( 12) hydrogen bonds : bond 0.18168 ( 279) hydrogen bonds : angle 5.66185 ( 792) metal coordination : bond 0.20276 ( 2) link_NAG-ASN : bond 0.00177 ( 1) link_NAG-ASN : angle 2.84613 ( 3) *********************** 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 : 0.244 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: 0.8246 (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: 0.4772 time to fit residues: 99.7070 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 : 0.251 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.0010 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 0.0970 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.2184 ------------------------------------------------------------------------------- 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 524 GLN A 598 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.123083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.111720 restraints weight = 9653.530| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.93 r_work: 0.3497 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6531 Z= 0.131 Angle : 0.560 6.922 8871 Z= 0.285 Chirality : 0.041 0.194 929 Planarity : 0.004 0.047 1144 Dihedral : 8.169 72.567 877 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.20 % Allowed : 15.27 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.31), residues: 776 helix: 1.18 (0.28), residues: 375 sheet: 2.07 (0.75), residues: 49 loop : -1.04 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 340 TYR 0.022 0.001 TYR A 183 PHE 0.025 0.001 PHE A 504 TRP 0.012 0.001 TRP B 353 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 6522) covalent geometry : angle 0.55440 ( 8856) SS BOND : bond 0.00143 ( 6) SS BOND : angle 1.98723 ( 12) hydrogen bonds : bond 0.05956 ( 279) hydrogen bonds : angle 4.17092 ( 792) metal coordination : bond 0.00312 ( 2) link_NAG-ASN : bond 0.00993 ( 1) link_NAG-ASN : angle 1.80539 ( 3) *********************** 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 181 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7363 (mp0) REVERT: A 74 GLU cc_start: 0.7928 (tp30) cc_final: 0.7506 (tp30) REVERT: A 75 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7700 (tm-30) REVERT: A 335 GLU cc_start: 0.8006 (tp30) cc_final: 0.7256 (mm-30) REVERT: A 470 LYS cc_start: 0.8383 (tppp) cc_final: 0.8101 (tppp) REVERT: A 509 ASP cc_start: 0.7027 (p0) cc_final: 0.6661 (p0) REVERT: A 564 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7466 (mp0) outliers start: 15 outliers final: 4 residues processed: 170 average time/residue: 0.5083 time to fit residues: 90.4451 Evaluate side-chains 167 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 161 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 383 MET 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 70 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 49 optimal weight: 0.0030 chunk 19 optimal weight: 0.0670 chunk 63 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 0.0980 chunk 39 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 overall best weight: 0.3128 ------------------------------------------------------------------------------- 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 401 HIS 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 = 0.3752 r_free = 0.3752 target = 0.122715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.111058 restraints weight = 9592.656| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.91 r_work: 0.3485 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6531 Z= 0.145 Angle : 0.542 7.734 8871 Z= 0.277 Chirality : 0.042 0.170 929 Planarity : 0.004 0.043 1144 Dihedral : 6.437 56.458 875 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.30), residues: 776 helix: 1.25 (0.28), residues: 374 sheet: 1.99 (0.75), residues: 49 loop : -1.14 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 340 TYR 0.020 0.001 TYR A 183 PHE 0.019 0.001 PHE A 28 TRP 0.011 0.001 TRP B 353 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 6522) covalent geometry : angle 0.53542 ( 8856) SS BOND : bond 0.00165 ( 6) SS BOND : angle 1.96206 ( 12) hydrogen bonds : bond 0.05848 ( 279) hydrogen bonds : angle 4.01881 ( 792) metal coordination : bond 0.00281 ( 2) link_NAG-ASN : bond 0.00841 ( 1) link_NAG-ASN : angle 2.80697 ( 3) *********************** 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 183 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7311 (mp0) REVERT: A 74 GLU cc_start: 0.7922 (tp30) cc_final: 0.7507 (tp30) REVERT: A 75 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7536 (tm-30) REVERT: A 335 GLU cc_start: 0.7890 (tp30) cc_final: 0.7206 (mm-30) REVERT: A 338 ASP cc_start: 0.7648 (p0) cc_final: 0.7346 (p0) REVERT: A 340 ARG cc_start: 0.8396 (mtm-85) cc_final: 0.8173 (mtm-85) REVERT: A 470 LYS cc_start: 0.8377 (tppp) cc_final: 0.8101 (tppp) REVERT: A 509 ASP cc_start: 0.7068 (p0) cc_final: 0.6734 (p0) REVERT: A 564 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: A 568 LEU cc_start: 0.8605 (tp) cc_final: 0.8377 (tt) REVERT: A 596 LYS cc_start: 0.8527 (mtmm) cc_final: 0.8114 (mtmm) outliers start: 18 outliers final: 5 residues processed: 167 average time/residue: 0.5048 time to fit residues: 88.4909 Evaluate side-chains 166 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 159 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 79 LEU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 564 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 0.0970 chunk 50 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 10 optimal weight: 0.0370 chunk 55 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 0.0770 overall best weight: 0.2214 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.123424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.111862 restraints weight = 9764.667| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.95 r_work: 0.3497 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6531 Z= 0.122 Angle : 0.546 9.068 8871 Z= 0.270 Chirality : 0.040 0.155 929 Planarity : 0.004 0.042 1144 Dihedral : 5.672 56.335 875 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.35 % Allowed : 19.09 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.31), residues: 776 helix: 1.38 (0.28), residues: 372 sheet: 1.87 (0.75), residues: 49 loop : -1.05 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 255 TYR 0.019 0.001 TYR A 183 PHE 0.015 0.001 PHE A 504 TRP 0.009 0.001 TRP A 477 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 6522) covalent geometry : angle 0.53884 ( 8856) SS BOND : bond 0.00132 ( 6) SS BOND : angle 1.81632 ( 12) hydrogen bonds : bond 0.05164 ( 279) hydrogen bonds : angle 3.89007 ( 792) metal coordination : bond 0.00190 ( 2) link_NAG-ASN : bond 0.00528 ( 1) link_NAG-ASN : angle 3.11977 ( 3) *********************** 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 177 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 377 PHE cc_start: 0.8235 (t80) cc_final: 0.8026 (t80) REVERT: A 30 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: A 74 GLU cc_start: 0.7924 (tp30) cc_final: 0.7500 (tp30) REVERT: A 75 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7753 (tm-30) REVERT: A 190 MET cc_start: 0.8180 (tmm) cc_final: 0.7698 (ttt) REVERT: A 335 GLU cc_start: 0.7894 (tp30) cc_final: 0.7190 (mm-30) REVERT: A 338 ASP cc_start: 0.7624 (p0) cc_final: 0.7250 (p0) REVERT: A 340 ARG cc_start: 0.8391 (mtm-85) cc_final: 0.8126 (mtm-85) REVERT: A 497 TYR cc_start: 0.7255 (m-10) cc_final: 0.7040 (m-10) REVERT: A 509 ASP cc_start: 0.7020 (p0) cc_final: 0.6687 (p0) REVERT: A 564 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7498 (mp0) outliers start: 16 outliers final: 5 residues processed: 166 average time/residue: 0.4653 time to fit residues: 80.9968 Evaluate side-chains 166 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 159 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 79 LEU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 564 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 63 optimal weight: 0.0470 chunk 64 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 7 optimal weight: 0.0170 chunk 23 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 chunk 66 optimal weight: 0.0770 chunk 70 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 overall best weight: 0.2074 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.123738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.112060 restraints weight = 9704.145| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.95 r_work: 0.3503 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6531 Z= 0.119 Angle : 0.545 7.788 8871 Z= 0.269 Chirality : 0.040 0.127 929 Planarity : 0.004 0.040 1144 Dihedral : 5.234 59.912 875 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.35 % Allowed : 19.24 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.31), residues: 776 helix: 1.39 (0.28), residues: 375 sheet: 1.84 (0.75), residues: 49 loop : -0.96 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 340 TYR 0.019 0.001 TYR A 183 PHE 0.014 0.001 PHE A 504 TRP 0.009 0.001 TRP A 477 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 6522) covalent geometry : angle 0.53759 ( 8856) SS BOND : bond 0.00208 ( 6) SS BOND : angle 1.78931 ( 12) hydrogen bonds : bond 0.04962 ( 279) hydrogen bonds : angle 3.82393 ( 792) metal coordination : bond 0.00185 ( 2) link_NAG-ASN : bond 0.00645 ( 1) link_NAG-ASN : angle 3.48507 ( 3) *********************** 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 176 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.272 Fit side-chains REVERT: B 365 TYR cc_start: 0.8513 (m-10) cc_final: 0.8132 (m-10) REVERT: B 369 TYR cc_start: 0.7370 (t80) cc_final: 0.7117 (t80) REVERT: B 377 PHE cc_start: 0.8215 (t80) cc_final: 0.7920 (t80) REVERT: A 30 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7157 (mp0) REVERT: A 66 GLU cc_start: 0.7951 (tp30) cc_final: 0.7520 (tp30) REVERT: A 74 GLU cc_start: 0.7926 (tp30) cc_final: 0.7501 (tp30) REVERT: A 75 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7733 (tm-30) REVERT: A 190 MET cc_start: 0.8117 (tmm) cc_final: 0.7617 (ttt) REVERT: A 238 GLU cc_start: 0.8013 (tt0) cc_final: 0.7680 (tm-30) REVERT: A 335 GLU cc_start: 0.7899 (tp30) cc_final: 0.7346 (mm-30) REVERT: A 338 ASP cc_start: 0.7612 (p0) cc_final: 0.7381 (p0) REVERT: A 509 ASP cc_start: 0.7017 (p0) cc_final: 0.6692 (p0) REVERT: A 564 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: A 596 LYS cc_start: 0.8484 (mtmm) cc_final: 0.8272 (mtmm) outliers start: 16 outliers final: 7 residues processed: 165 average time/residue: 0.4326 time to fit residues: 75.1395 Evaluate side-chains 166 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 157 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 85 SER 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 462 MET Chi-restraints excluded: chain A residue 564 GLU 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 66 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 0.4980 chunk 6 optimal weight: 0.2980 chunk 19 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 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 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 = 0.3720 r_free = 0.3720 target = 0.120146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.108665 restraints weight = 9664.232| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.93 r_work: 0.3451 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2163 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= 0.203 Angle : 0.606 8.014 8871 Z= 0.307 Chirality : 0.043 0.139 929 Planarity : 0.004 0.041 1144 Dihedral : 5.106 55.504 875 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.20 % Allowed : 21.73 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.31), residues: 776 helix: 1.31 (0.28), residues: 375 sheet: 1.93 (0.76), residues: 49 loop : -1.17 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 340 TYR 0.024 0.002 TYR A 183 PHE 0.015 0.002 PHE A 504 TRP 0.014 0.002 TRP A 477 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 6522) covalent geometry : angle 0.59591 ( 8856) SS BOND : bond 0.00315 ( 6) SS BOND : angle 2.18075 ( 12) hydrogen bonds : bond 0.06694 ( 279) hydrogen bonds : angle 4.01521 ( 792) metal coordination : bond 0.00505 ( 2) link_NAG-ASN : bond 0.00334 ( 1) link_NAG-ASN : angle 4.13622 ( 3) *********************** 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 184 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 377 PHE cc_start: 0.8444 (t80) cc_final: 0.8162 (t80) REVERT: A 30 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: A 74 GLU cc_start: 0.7906 (tp30) cc_final: 0.7684 (tp30) REVERT: A 75 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7573 (tm-30) REVERT: A 190 MET cc_start: 0.8193 (tmm) cc_final: 0.7714 (ttt) REVERT: A 335 GLU cc_start: 0.7868 (tp30) cc_final: 0.7206 (mm-30) REVERT: A 338 ASP cc_start: 0.7668 (p0) cc_final: 0.7409 (p0) REVERT: A 509 ASP cc_start: 0.7247 (p0) cc_final: 0.6912 (p0) REVERT: A 564 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: A 596 LYS cc_start: 0.8524 (mtmm) cc_final: 0.8275 (mtmm) outliers start: 15 outliers final: 9 residues processed: 174 average time/residue: 0.4750 time to fit residues: 86.7650 Evaluate side-chains 172 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 85 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 462 MET Chi-restraints excluded: chain A residue 564 GLU 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 29 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 4 optimal weight: 0.2980 chunk 33 optimal weight: 0.2980 chunk 70 optimal weight: 0.5980 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 42 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 = 0.3729 r_free = 0.3729 target = 0.120809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.109336 restraints weight = 9661.069| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.93 r_work: 0.3462 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6531 Z= 0.171 Angle : 0.597 8.940 8871 Z= 0.302 Chirality : 0.042 0.156 929 Planarity : 0.004 0.042 1144 Dihedral : 4.860 49.992 875 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.20 % Allowed : 21.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.31), residues: 776 helix: 1.37 (0.28), residues: 369 sheet: 1.94 (0.75), residues: 49 loop : -1.20 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 340 TYR 0.022 0.002 TYR A 183 PHE 0.022 0.001 PHE A 28 TRP 0.012 0.001 TRP B 353 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 6522) covalent geometry : angle 0.58667 ( 8856) SS BOND : bond 0.00189 ( 6) SS BOND : angle 2.14135 ( 12) hydrogen bonds : bond 0.06154 ( 279) hydrogen bonds : angle 4.01489 ( 792) metal coordination : bond 0.00380 ( 2) link_NAG-ASN : bond 0.00174 ( 1) link_NAG-ASN : angle 4.43443 ( 3) *********************** 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 182 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 350 VAL cc_start: 0.8116 (t) cc_final: 0.7857 (p) REVERT: B 365 TYR cc_start: 0.8542 (m-10) cc_final: 0.8177 (m-10) REVERT: B 377 PHE cc_start: 0.8361 (t80) cc_final: 0.8121 (t80) REVERT: A 30 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: A 66 GLU cc_start: 0.7991 (tp30) cc_final: 0.7499 (tp30) REVERT: A 74 GLU cc_start: 0.7918 (tp30) cc_final: 0.7662 (tp30) REVERT: A 75 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7604 (tm-30) REVERT: A 190 MET cc_start: 0.8191 (tmm) cc_final: 0.7704 (ttt) REVERT: A 238 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7803 (tt0) REVERT: A 335 GLU cc_start: 0.7879 (tp30) cc_final: 0.7281 (mm-30) REVERT: A 394 ASN cc_start: 0.7898 (m-40) cc_final: 0.7645 (m110) REVERT: A 509 ASP cc_start: 0.7120 (p0) cc_final: 0.6814 (p0) REVERT: A 564 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: A 596 LYS cc_start: 0.8537 (mtmm) cc_final: 0.8291 (mtmm) outliers start: 15 outliers final: 7 residues processed: 169 average time/residue: 0.4923 time to fit residues: 87.2544 Evaluate side-chains 173 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 85 SER Chi-restraints excluded: chain A residue 238 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 462 MET Chi-restraints excluded: chain A residue 564 GLU 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 15 optimal weight: 1.9990 chunk 7 optimal weight: 0.0030 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 10 optimal weight: 0.2980 chunk 65 optimal weight: 0.8980 overall best weight: 0.4590 ------------------------------------------------------------------------------- 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 42 GLN A 175 GLN A 572 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.120106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.108797 restraints weight = 9599.273| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.91 r_work: 0.3456 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6531 Z= 0.192 Angle : 0.619 8.082 8871 Z= 0.316 Chirality : 0.043 0.164 929 Planarity : 0.004 0.043 1144 Dihedral : 4.839 48.408 875 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.64 % Allowed : 21.29 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.31), residues: 776 helix: 1.39 (0.28), residues: 369 sheet: 1.98 (0.75), residues: 49 loop : -1.27 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 340 TYR 0.022 0.002 TYR A 183 PHE 0.027 0.002 PHE A 28 TRP 0.012 0.002 TRP A 477 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 6522) covalent geometry : angle 0.60737 ( 8856) SS BOND : bond 0.00223 ( 6) SS BOND : angle 2.22229 ( 12) hydrogen bonds : bond 0.06550 ( 279) hydrogen bonds : angle 4.03343 ( 792) metal coordination : bond 0.00445 ( 2) link_NAG-ASN : bond 0.00102 ( 1) link_NAG-ASN : angle 4.75782 ( 3) *********************** 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 184 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: B 350 VAL cc_start: 0.8136 (t) cc_final: 0.7895 (p) REVERT: B 377 PHE cc_start: 0.8403 (t80) cc_final: 0.8179 (t80) REVERT: B 408 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8189 (ptm-80) REVERT: A 30 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: A 74 GLU cc_start: 0.7911 (tp30) cc_final: 0.7692 (tp30) REVERT: A 75 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7636 (tm-30) REVERT: A 190 MET cc_start: 0.8203 (tmm) cc_final: 0.7747 (ttt) REVERT: A 335 GLU cc_start: 0.7869 (tp30) cc_final: 0.7248 (mm-30) REVERT: A 394 ASN cc_start: 0.7873 (m-40) cc_final: 0.7627 (m-40) REVERT: A 509 ASP cc_start: 0.7231 (p0) cc_final: 0.6913 (p0) REVERT: A 556 ASN cc_start: 0.8689 (t0) cc_final: 0.8487 (t0) REVERT: A 564 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: A 596 LYS cc_start: 0.8537 (mtmm) cc_final: 0.8325 (mtmm) outliers start: 18 outliers final: 8 residues processed: 175 average time/residue: 0.5030 time to fit residues: 92.5177 Evaluate side-chains 169 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 85 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 462 MET Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 611 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 47 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 42 optimal weight: 0.5980 chunk 25 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN A 42 GLN A 175 GLN A 401 HIS A 493 HIS A 572 ASN A 598 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.120044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.108595 restraints weight = 9618.509| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.94 r_work: 0.3447 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6531 Z= 0.210 Angle : 0.641 9.471 8871 Z= 0.324 Chirality : 0.044 0.166 929 Planarity : 0.004 0.043 1144 Dihedral : 4.881 48.330 875 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.91 % Allowed : 22.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.30), residues: 776 helix: 1.26 (0.28), residues: 371 sheet: 1.95 (0.75), residues: 49 loop : -1.32 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 340 TYR 0.024 0.002 TYR A 183 PHE 0.029 0.002 PHE A 28 TRP 0.013 0.002 TRP A 477 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 6522) covalent geometry : angle 0.62922 ( 8856) SS BOND : bond 0.00241 ( 6) SS BOND : angle 2.32078 ( 12) hydrogen bonds : bond 0.06808 ( 279) hydrogen bonds : angle 4.07680 ( 792) metal coordination : bond 0.00496 ( 2) link_NAG-ASN : bond 0.00009 ( 1) link_NAG-ASN : angle 5.01327 ( 3) *********************** 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 178 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 350 VAL cc_start: 0.8170 (t) cc_final: 0.7931 (p) REVERT: B 365 TYR cc_start: 0.8531 (m-10) cc_final: 0.8174 (m-10) REVERT: B 377 PHE cc_start: 0.8418 (t80) cc_final: 0.8175 (t80) REVERT: B 524 VAL cc_start: 0.7578 (OUTLIER) cc_final: 0.7316 (p) REVERT: A 30 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: A 74 GLU cc_start: 0.7963 (tp30) cc_final: 0.7743 (tp30) REVERT: A 75 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7659 (tm-30) REVERT: A 190 MET cc_start: 0.8243 (tmm) cc_final: 0.7803 (ttt) REVERT: A 335 GLU cc_start: 0.7857 (tp30) cc_final: 0.7244 (mm-30) REVERT: A 394 ASN cc_start: 0.7921 (m-40) cc_final: 0.7655 (m-40) REVERT: A 509 ASP cc_start: 0.7237 (p0) cc_final: 0.6925 (p0) REVERT: A 556 ASN cc_start: 0.8705 (t0) cc_final: 0.8484 (t0) REVERT: A 564 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7598 (mp0) outliers start: 13 outliers final: 10 residues processed: 170 average time/residue: 0.4892 time to fit residues: 87.2878 Evaluate side-chains 174 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 85 SER Chi-restraints excluded: chain A residue 175 GLN 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 462 MET Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 611 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 53 optimal weight: 0.6980 chunk 72 optimal weight: 0.0270 chunk 65 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 0.0870 chunk 39 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 17 optimal weight: 0.0570 overall best weight: 0.2134 ------------------------------------------------------------------------------- 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 42 GLN A 175 GLN 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 = 0.3756 r_free = 0.3756 target = 0.122777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.111314 restraints weight = 9667.773| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.93 r_work: 0.3494 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6531 Z= 0.128 Angle : 0.593 9.310 8871 Z= 0.299 Chirality : 0.041 0.166 929 Planarity : 0.004 0.044 1144 Dihedral : 4.554 42.816 875 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.06 % Allowed : 23.05 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.31), residues: 776 helix: 1.53 (0.28), residues: 366 sheet: 1.90 (0.76), residues: 49 loop : -1.21 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 340 TYR 0.023 0.001 TYR A 183 PHE 0.025 0.001 PHE A 28 TRP 0.016 0.001 TRP A 165 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 6522) covalent geometry : angle 0.58210 ( 8856) SS BOND : bond 0.00135 ( 6) SS BOND : angle 2.06203 ( 12) hydrogen bonds : bond 0.05343 ( 279) hydrogen bonds : angle 3.93695 ( 792) metal coordination : bond 0.00194 ( 2) link_NAG-ASN : bond 0.00104 ( 1) link_NAG-ASN : angle 4.60333 ( 3) ********************** 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 176 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: B 365 TYR cc_start: 0.8522 (m-10) cc_final: 0.8147 (m-10) REVERT: B 524 VAL cc_start: 0.7502 (OUTLIER) cc_final: 0.7222 (p) REVERT: A 30 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7141 (mp0) REVERT: A 74 GLU cc_start: 0.7885 (tp30) cc_final: 0.7461 (tp30) REVERT: A 75 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7745 (tm-30) REVERT: A 190 MET cc_start: 0.8184 (tmm) cc_final: 0.7715 (ttt) REVERT: A 333 LEU cc_start: 0.8621 (mm) cc_final: 0.8398 (mt) REVERT: A 335 GLU cc_start: 0.7887 (tp30) cc_final: 0.7289 (mm-30) REVERT: A 394 ASN cc_start: 0.7761 (m-40) cc_final: 0.7474 (m-40) REVERT: A 509 ASP cc_start: 0.7064 (p0) cc_final: 0.6757 (p0) REVERT: A 556 ASN cc_start: 0.8714 (t0) cc_final: 0.8493 (t0) REVERT: A 564 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: A 596 LYS cc_start: 0.8515 (mtmt) cc_final: 0.8273 (mtmm) outliers start: 14 outliers final: 9 residues processed: 167 average time/residue: 0.5001 time to fit residues: 87.7828 Evaluate side-chains 170 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 262 LEU 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 462 MET Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 611 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 9 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 53 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 68 optimal weight: 0.1980 chunk 18 optimal weight: 0.0980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN A 175 GLN 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 = 0.3726 r_free = 0.3726 target = 0.120525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.109151 restraints weight = 9671.104| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.93 r_work: 0.3462 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6531 Z= 0.179 Angle : 0.627 9.768 8871 Z= 0.313 Chirality : 0.043 0.172 929 Planarity : 0.004 0.043 1144 Dihedral : 4.721 45.438 875 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.20 % Allowed : 23.49 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.31), residues: 776 helix: 1.44 (0.28), residues: 369 sheet: 1.96 (0.74), residues: 49 loop : -1.27 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 559 TYR 0.023 0.002 TYR A 183 PHE 0.028 0.002 PHE A 28 TRP 0.021 0.002 TRP A 165 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 6522) covalent geometry : angle 0.61520 ( 8856) SS BOND : bond 0.00212 ( 6) SS BOND : angle 2.19820 ( 12) hydrogen bonds : bond 0.06258 ( 279) hydrogen bonds : angle 3.96766 ( 792) metal coordination : bond 0.00439 ( 2) link_NAG-ASN : bond 0.00079 ( 1) link_NAG-ASN : angle 4.92939 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2590.35 seconds wall clock time: 44 minutes 40.06 seconds (2680.06 seconds total)