Starting phenix.real_space_refine on Tue Mar 11 17:20:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wox_37701/03_2025/8wox_37701.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wox_37701/03_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_37701/03_2025/8wox_37701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wox_37701/03_2025/8wox_37701.map" model { file = "/net/cci-nas-00/data/ceres_data/8wox_37701/03_2025/8wox_37701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wox_37701/03_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-5624/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: 7.11, per 1000 atoms: 1.12 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: 1.56 Conformation dependent library (CDL) restraints added in 844.7 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: 0.59 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: 1.93 Time building geometry restraints manager: 1.87 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: 4.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.410 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:14.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.060 ------------------------------------------------------------------------------- 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 : 0.003 0.026 6522 Z= 0.199 Angle : 0.530 6.152 8856 Z= 0.292 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 *********************** 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 : 0.646 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: 1.1411 time to fit residues: 238.7475 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 : 0.735 ------------------------------------------------------------------------------- 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 6522 Z= 0.280 Angle : 0.597 7.036 8856 Z= 0.309 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 *********************** 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 : 0.646 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: 1.1401 time to fit residues: 211.8942 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 : 0.772 ------------------------------------------------------------------------------- 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 6522 Z= 0.278 Angle : 0.568 8.245 8856 Z= 0.295 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 *********************** 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 : 0.660 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: 1.1529 time to fit residues: 210.5920 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 : 0.738 ------------------------------------------------------------------------------- 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: 0.0040 chunk 51 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 57 optimal weight: 0.2980 chunk 35 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 25 optimal weight: 0.3980 chunk 46 optimal weight: 0.9980 overall best weight: 0.4392 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.120149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.108731 restraints weight = 9809.187| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.93 r_work: 0.3451 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6522 Z= 0.268 Angle : 0.576 7.401 8856 Z= 0.293 Chirality : 0.043 0.165 929 Planarity : 0.004 0.044 1144 Dihedral : 5.712 52.966 875 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.50 % Allowed : 19.38 % Favored : 78.12 % 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: 0.20 (0.31), residues: 776 helix: 1.10 (0.28), residues: 376 sheet: 2.00 (0.75), residues: 49 loop : -1.25 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 353 HIS 0.005 0.001 HIS A 241 PHE 0.020 0.002 PHE A 28 TYR 0.023 0.002 TYR A 183 ARG 0.007 0.000 ARG A 340 *********************** 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: 17 poor density : 163 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 524 VAL cc_start: 0.7396 (OUTLIER) cc_final: 0.7156 (p) REVERT: A 30 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: A 74 GLU cc_start: 0.7916 (tp30) cc_final: 0.7465 (tp30) REVERT: A 75 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7649 (tm-30) REVERT: A 238 GLU cc_start: 0.8041 (tt0) cc_final: 0.7822 (tt0) REVERT: A 334 THR cc_start: 0.8600 (t) cc_final: 0.8375 (m) REVERT: A 335 GLU cc_start: 0.8051 (tp30) cc_final: 0.7303 (mm-30) REVERT: A 455 MET cc_start: 0.8073 (tmm) cc_final: 0.7852 (tmm) REVERT: A 509 ASP cc_start: 0.7234 (p0) cc_final: 0.6917 (p0) REVERT: A 564 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: A 596 LYS cc_start: 0.8532 (mtmm) cc_final: 0.8304 (mtmm) outliers start: 17 outliers final: 7 residues processed: 168 average time/residue: 1.1566 time to fit residues: 204.3592 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 : 0.655 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 54 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 53 optimal weight: 0.1980 chunk 44 optimal weight: 0.0000 chunk 23 optimal weight: 1.9990 chunk 40 optimal weight: 0.0870 chunk 51 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 overall best weight: 0.3762 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.120570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.109281 restraints weight = 9594.175| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.91 r_work: 0.3461 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6522 Z= 0.239 Angle : 0.568 9.839 8856 Z= 0.288 Chirality : 0.042 0.127 929 Planarity : 0.004 0.045 1144 Dihedral : 5.388 58.336 875 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.23 % Allowed : 19.38 % Favored : 77.39 % 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: 0.26 (0.31), residues: 776 helix: 1.18 (0.28), residues: 375 sheet: 1.99 (0.75), residues: 49 loop : -1.24 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 353 HIS 0.005 0.001 HIS A 241 PHE 0.020 0.001 PHE A 28 TYR 0.023 0.001 TYR A 183 ARG 0.005 0.000 ARG A 340 *********************** 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 193 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: A 74 GLU cc_start: 0.7901 (tp30) cc_final: 0.7479 (tp30) REVERT: A 75 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7633 (tm-30) REVERT: A 190 MET cc_start: 0.8165 (tmm) cc_final: 0.7708 (ttt) REVERT: A 238 GLU cc_start: 0.8004 (tt0) cc_final: 0.7794 (tt0) REVERT: A 334 THR cc_start: 0.8598 (t) cc_final: 0.8383 (m) REVERT: A 335 GLU cc_start: 0.8040 (tp30) cc_final: 0.7313 (mm-30) REVERT: A 455 MET cc_start: 0.8046 (tmm) cc_final: 0.7834 (tmm) REVERT: A 509 ASP cc_start: 0.7117 (p0) cc_final: 0.6802 (p0) REVERT: A 564 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: A 568 LEU cc_start: 0.8644 (tp) cc_final: 0.8441 (tt) outliers start: 22 outliers final: 11 residues processed: 177 average time/residue: 1.0390 time to fit residues: 194.0994 Evaluate side-chains 175 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 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 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 58 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 chunk 56 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.118058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.106988 restraints weight = 9458.150| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.90 r_work: 0.3428 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 6522 Z= 0.394 Angle : 0.640 8.114 8856 Z= 0.329 Chirality : 0.046 0.135 929 Planarity : 0.005 0.046 1144 Dihedral : 5.433 59.251 875 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.52 % Allowed : 19.82 % Favored : 76.65 % 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: 0.08 (0.30), residues: 776 helix: 1.14 (0.28), residues: 372 sheet: 1.68 (0.74), residues: 51 loop : -1.44 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 477 HIS 0.007 0.002 HIS A 241 PHE 0.026 0.002 PHE A 28 TYR 0.027 0.002 TYR A 587 ARG 0.007 0.001 ARG A 340 *********************** 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 193 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: B 350 VAL cc_start: 0.8211 (t) cc_final: 0.7931 (p) REVERT: B 408 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8170 (ptm-80) REVERT: A 30 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7394 (mp0) REVERT: A 74 GLU cc_start: 0.7966 (tp30) cc_final: 0.7747 (tp30) REVERT: A 75 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7666 (tm-30) REVERT: A 190 MET cc_start: 0.8168 (tmm) cc_final: 0.7736 (ttt) REVERT: A 238 GLU cc_start: 0.7998 (tt0) cc_final: 0.7784 (tt0) REVERT: A 335 GLU cc_start: 0.8027 (tp30) cc_final: 0.7393 (mm-30) REVERT: A 435 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7251 (mt-10) REVERT: A 455 MET cc_start: 0.8045 (tmm) cc_final: 0.7701 (tmm) REVERT: A 509 ASP cc_start: 0.7309 (p0) cc_final: 0.7005 (p0) REVERT: A 525 PHE cc_start: 0.8507 (m-10) cc_final: 0.8302 (m-10) REVERT: A 564 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: A 568 LEU cc_start: 0.8652 (tp) cc_final: 0.8429 (tt) REVERT: A 592 PHE cc_start: 0.8042 (t80) cc_final: 0.7839 (t80) outliers start: 24 outliers final: 13 residues processed: 179 average time/residue: 1.0696 time to fit residues: 201.7366 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 : 0.712 ------------------------------------------------------------------------------- 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 195 ASN Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 313 LYS 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 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 611 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 0.3980 chunk 52 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 20 optimal weight: 0.2980 chunk 25 optimal weight: 0.8980 chunk 47 optimal weight: 0.1980 chunk 29 optimal weight: 0.2980 chunk 5 optimal weight: 0.3980 chunk 3 optimal weight: 0.2980 chunk 0 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 overall best weight: 0.2980 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.121282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.109873 restraints weight = 9499.084| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.93 r_work: 0.3465 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6522 Z= 0.216 Angle : 0.592 9.254 8856 Z= 0.300 Chirality : 0.041 0.140 929 Planarity : 0.004 0.046 1144 Dihedral : 4.883 50.018 875 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.11 % Allowed : 19.68 % 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: 0.33 (0.31), residues: 776 helix: 1.31 (0.28), residues: 371 sheet: 1.72 (0.76), residues: 51 loop : -1.23 (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 0.021 0.001 PHE A 28 TYR 0.022 0.001 TYR A 183 ARG 0.007 0.000 ARG A 340 *********************** 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 194 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 350 VAL cc_start: 0.8156 (t) cc_final: 0.7876 (p) REVERT: B 365 TYR cc_start: 0.8524 (m-10) cc_final: 0.8204 (m-10) REVERT: A 30 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: A 74 GLU cc_start: 0.7905 (tp30) cc_final: 0.7478 (tp30) REVERT: A 75 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7714 (tm-30) REVERT: A 190 MET cc_start: 0.8196 (tmm) cc_final: 0.7714 (ttt) REVERT: A 238 GLU cc_start: 0.7977 (tt0) cc_final: 0.7760 (tt0) REVERT: A 335 GLU cc_start: 0.8082 (tp30) cc_final: 0.7593 (mm-30) REVERT: A 435 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7211 (mt-10) REVERT: A 509 ASP cc_start: 0.7114 (p0) cc_final: 0.6801 (p0) REVERT: A 564 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: A 568 LEU cc_start: 0.8635 (tp) cc_final: 0.8383 (tt) outliers start: 28 outliers final: 15 residues processed: 178 average time/residue: 1.1285 time to fit residues: 211.7047 Evaluate side-chains 180 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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 195 ASN Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 313 LYS 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 512 PHE 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 64 optimal weight: 0.0970 chunk 39 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 10 optimal weight: 0.0770 chunk 46 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 51 optimal weight: 0.0470 overall best weight: 0.2634 ------------------------------------------------------------------------------- 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 493 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 = 0.3745 r_free = 0.3745 target = 0.122334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.110925 restraints weight = 9460.866| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.90 r_work: 0.3483 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6522 Z= 0.199 Angle : 0.588 8.769 8856 Z= 0.295 Chirality : 0.041 0.128 929 Planarity : 0.004 0.045 1144 Dihedral : 4.665 46.213 875 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.08 % Allowed : 21.44 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.45 (0.31), residues: 776 helix: 1.46 (0.28), residues: 368 sheet: 1.69 (0.75), residues: 51 loop : -1.20 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.004 0.001 HIS A 241 PHE 0.022 0.001 PHE A 28 TYR 0.023 0.001 TYR A 183 ARG 0.007 0.000 ARG A 340 *********************** 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 186 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 365 TYR cc_start: 0.8537 (m-10) cc_final: 0.8166 (m-10) REVERT: A 30 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7147 (mp0) REVERT: A 66 GLU cc_start: 0.7951 (tp30) cc_final: 0.7726 (tp30) REVERT: A 74 GLU cc_start: 0.7929 (tp30) cc_final: 0.7514 (tp30) REVERT: A 75 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7719 (tm-30) REVERT: A 190 MET cc_start: 0.8193 (tmm) cc_final: 0.7700 (ttt) REVERT: A 238 GLU cc_start: 0.7990 (tt0) cc_final: 0.7788 (tt0) REVERT: A 335 GLU cc_start: 0.8118 (tp30) cc_final: 0.7460 (mm-30) REVERT: A 509 ASP cc_start: 0.7133 (p0) cc_final: 0.6809 (p0) REVERT: A 564 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: A 568 LEU cc_start: 0.8622 (tp) cc_final: 0.8404 (tt) REVERT: A 596 LYS cc_start: 0.8453 (mtmm) cc_final: 0.8200 (mttm) outliers start: 21 outliers final: 15 residues processed: 171 average time/residue: 1.0821 time to fit residues: 195.0269 Evaluate side-chains 179 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 195 ASN Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 313 LYS 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 462 MET Chi-restraints excluded: chain A residue 512 PHE 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 72 optimal weight: 0.0770 chunk 74 optimal weight: 0.0060 chunk 31 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 46 optimal weight: 0.0870 chunk 1 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 47 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 overall best weight: 0.2732 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.122377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.110956 restraints weight = 9495.867| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.91 r_work: 0.3485 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6522 Z= 0.203 Angle : 0.586 9.538 8856 Z= 0.295 Chirality : 0.041 0.160 929 Planarity : 0.004 0.045 1144 Dihedral : 4.603 44.864 875 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.94 % Allowed : 21.44 % Favored : 75.62 % 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: 0.47 (0.31), residues: 776 helix: 1.50 (0.28), residues: 367 sheet: 1.65 (0.75), residues: 51 loop : -1.20 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 165 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 0.004 0.000 ARG A 559 *********************** 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 182 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: B 365 TYR cc_start: 0.8539 (m-10) cc_final: 0.8183 (m-10) REVERT: B 408 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8196 (ptm-80) REVERT: A 30 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: A 66 GLU cc_start: 0.7955 (tp30) cc_final: 0.7718 (tp30) REVERT: A 74 GLU cc_start: 0.7927 (tp30) cc_final: 0.7511 (tp30) REVERT: A 75 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7734 (tm-30) REVERT: A 190 MET cc_start: 0.8190 (tmm) cc_final: 0.7674 (ttt) REVERT: A 238 GLU cc_start: 0.7971 (tt0) cc_final: 0.7770 (tt0) REVERT: A 335 GLU cc_start: 0.7958 (tp30) cc_final: 0.7381 (mm-30) REVERT: A 338 ASP cc_start: 0.7889 (p0) cc_final: 0.7676 (p0) REVERT: A 470 LYS cc_start: 0.8546 (tppp) cc_final: 0.8332 (tppp) REVERT: A 509 ASP cc_start: 0.7142 (p0) cc_final: 0.6818 (p0) REVERT: A 564 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: A 596 LYS cc_start: 0.8466 (mtmm) cc_final: 0.8215 (mttm) outliers start: 20 outliers final: 13 residues processed: 169 average time/residue: 1.0783 time to fit residues: 192.5426 Evaluate side-chains 174 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 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 313 LYS 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 411 SER 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 611 THR 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: 0.4980 chunk 67 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 A 598 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.119467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.108156 restraints weight = 9647.269| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.94 r_work: 0.3443 rms_B_bonded: 2.44 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: 0.8040 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6522 Z= 0.315 Angle : 0.642 9.550 8856 Z= 0.325 Chirality : 0.045 0.193 929 Planarity : 0.005 0.045 1144 Dihedral : 4.907 48.127 875 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.64 % Allowed : 23.05 % 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 (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: 0.24 (0.30), residues: 776 helix: 1.33 (0.28), residues: 372 sheet: 1.67 (0.74), residues: 51 loop : -1.41 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 165 HIS 0.006 0.001 HIS A 241 PHE 0.028 0.002 PHE A 28 TYR 0.025 0.002 TYR A 183 ARG 0.007 0.001 ARG A 340 ********************** 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 183 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: B 350 VAL cc_start: 0.8125 (t) cc_final: 0.7865 (p) REVERT: A 30 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: A 66 GLU cc_start: 0.7948 (tp30) cc_final: 0.7675 (tp30) REVERT: A 74 GLU cc_start: 0.7936 (tp30) cc_final: 0.7483 (tp30) REVERT: A 75 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7660 (tm-30) REVERT: A 190 MET cc_start: 0.8228 (tmm) cc_final: 0.7738 (ttt) REVERT: A 238 GLU cc_start: 0.7994 (tt0) cc_final: 0.7790 (tt0) REVERT: A 333 LEU cc_start: 0.8710 (mm) cc_final: 0.8499 (mt) REVERT: A 335 GLU cc_start: 0.7923 (tp30) cc_final: 0.7371 (mm-30) REVERT: A 470 LYS cc_start: 0.8553 (tppp) cc_final: 0.8339 (tppp) REVERT: A 509 ASP cc_start: 0.7239 (p0) cc_final: 0.6930 (p0) REVERT: A 556 ASN cc_start: 0.8713 (t0) cc_final: 0.8493 (t0) REVERT: A 564 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: A 596 LYS cc_start: 0.8488 (mtmm) cc_final: 0.8238 (mttm) outliers start: 18 outliers final: 14 residues processed: 171 average time/residue: 1.1023 time to fit residues: 198.2768 Evaluate side-chains 178 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 195 ASN Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 313 LYS 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 411 SER 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 611 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 36 optimal weight: 0.0770 chunk 34 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 76 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 59 optimal weight: 0.2980 chunk 72 optimal weight: 0.9980 chunk 16 optimal weight: 0.0470 chunk 40 optimal weight: 0.1980 overall best weight: 0.1836 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.123893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.112238 restraints weight = 9759.721| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.95 r_work: 0.3503 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6522 Z= 0.176 Angle : 0.587 9.088 8856 Z= 0.295 Chirality : 0.041 0.166 929 Planarity : 0.004 0.045 1144 Dihedral : 4.475 41.208 875 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.20 % Allowed : 23.20 % 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: 0.43 (0.31), residues: 776 helix: 1.47 (0.28), residues: 370 sheet: 1.67 (0.74), residues: 51 loop : -1.27 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 PHE 0.024 0.001 PHE A 28 TYR 0.023 0.001 TYR A 183 ARG 0.008 0.000 ARG A 340 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5947.81 seconds wall clock time: 101 minutes 42.72 seconds (6102.72 seconds total)