Starting phenix.real_space_refine on Mon Mar 11 00:36:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wox_37701/03_2024/8wox_37701.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wox_37701/03_2024/8wox_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wox_37701/03_2024/8wox_37701.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wox_37701/03_2024/8wox_37701.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wox_37701/03_2024/8wox_37701.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wox_37701/03_2024/8wox_37701.pdb" } 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 Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.03, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 2.23 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.66 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: 1.62 Time building geometry restraints manager: 2.46 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: 100.55 - 107.24: 218 107.24 - 113.92: 3463 113.92 - 120.60: 2816 120.60 - 127.29: 2273 127.29 - 133.97: 86 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 2.440 nonbonded pdb=" OG SER A 331 " pdb=" O ILE A 358 " model vdw 2.247 2.440 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.250 2.520 ... (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 ========== 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: 6.760 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: 22.180 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.220 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:15.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.710 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 0.746 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: 1.1071 time to fit residues: 231.5396 Evaluate side-chains 169 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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: 0.8980 chunk 58 optimal weight: 0.4980 chunk 32 optimal weight: 0.2980 chunk 19 optimal weight: 0.0570 chunk 39 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 69 optimal weight: 0.6980 overall best weight: 0.3298 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6522 Z= 0.221 Angle : 0.565 7.056 8856 Z= 0.289 Chirality : 0.042 0.207 929 Planarity : 0.004 0.045 1144 Dihedral : 7.983 69.521 877 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.94 % Allowed : 15.42 % Favored : 81.64 % 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: 0.27 (0.31), residues: 776 helix: 1.12 (0.28), residues: 376 sheet: 2.24 (0.76), residues: 49 loop : -1.19 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 353 HIS 0.006 0.001 HIS A 241 PHE 0.026 0.002 PHE A 504 TYR 0.023 0.001 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 193 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 173 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 408 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7940 (ptm-80) REVERT: A 30 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: A 74 GLU cc_start: 0.7578 (tp30) cc_final: 0.7166 (tp30) REVERT: A 75 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7448 (tm-30) REVERT: A 334 THR cc_start: 0.8495 (t) cc_final: 0.8265 (m) REVERT: A 335 GLU cc_start: 0.7710 (tp30) cc_final: 0.7023 (mm-30) REVERT: A 338 ASP cc_start: 0.7368 (p0) cc_final: 0.7053 (p0) REVERT: A 340 ARG cc_start: 0.8015 (mtm-85) cc_final: 0.7692 (mtm-85) REVERT: A 455 MET cc_start: 0.8249 (tmm) cc_final: 0.8038 (tmm) REVERT: A 470 LYS cc_start: 0.8210 (tppp) cc_final: 0.7926 (tppp) REVERT: A 509 ASP cc_start: 0.6911 (p0) cc_final: 0.6534 (p0) REVERT: A 572 ASN cc_start: 0.8362 (m-40) cc_final: 0.8094 (m110) outliers start: 20 outliers final: 7 residues processed: 180 average time/residue: 1.1488 time to fit residues: 217.0988 Evaluate side-chains 175 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 166 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 B residue 427 ASP 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 608 THR Chi-restraints excluded: chain A residue 611 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 19 optimal weight: 0.0770 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 62 optimal weight: 0.3980 chunk 69 optimal weight: 0.0980 chunk 23 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN A 101 GLN A 598 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6522 Z= 0.220 Angle : 0.539 7.774 8856 Z= 0.275 Chirality : 0.041 0.147 929 Planarity : 0.004 0.043 1144 Dihedral : 6.454 55.682 875 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.79 % Allowed : 19.09 % 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: 0.34 (0.31), residues: 776 helix: 1.23 (0.28), residues: 374 sheet: 2.19 (0.76), residues: 49 loop : -1.21 (0.32), residues: 353 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 0.018 0.001 PHE A 504 TYR 0.021 0.001 TYR A 183 ARG 0.004 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 fitting. rotamer outliers: 19 poor density : 166 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6982 (mp0) REVERT: A 74 GLU cc_start: 0.7582 (tp30) cc_final: 0.7165 (tp30) REVERT: A 75 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7456 (tm-30) REVERT: A 334 THR cc_start: 0.8516 (t) cc_final: 0.8274 (m) REVERT: A 335 GLU cc_start: 0.7724 (tp30) cc_final: 0.6959 (mm-30) REVERT: A 338 ASP cc_start: 0.7343 (p0) cc_final: 0.7123 (p0) REVERT: A 341 LYS cc_start: 0.7909 (mttt) cc_final: 0.7623 (mttt) REVERT: A 455 MET cc_start: 0.8240 (tmm) cc_final: 0.8024 (tmm) REVERT: A 483 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7350 (tp30) REVERT: A 509 ASP cc_start: 0.6983 (p0) cc_final: 0.6614 (p0) REVERT: A 564 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: A 568 LEU cc_start: 0.8655 (tp) cc_final: 0.8411 (tt) REVERT: A 572 ASN cc_start: 0.8361 (m-40) cc_final: 0.8041 (m110) REVERT: A 596 LYS cc_start: 0.8387 (mtmm) cc_final: 0.8158 (mtmm) outliers start: 19 outliers final: 7 residues processed: 172 average time/residue: 1.1561 time to fit residues: 209.2026 Evaluate side-chains 167 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 158 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 427 ASP 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 365 THR Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 611 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 7 optimal weight: 0.0060 chunk 33 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN A 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6522 Z= 0.407 Angle : 0.636 8.955 8856 Z= 0.328 Chirality : 0.047 0.182 929 Planarity : 0.005 0.045 1144 Dihedral : 5.715 49.270 875 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.82 % Allowed : 19.24 % Favored : 76.95 % 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: 0.98 (0.28), residues: 378 sheet: 2.05 (0.75), residues: 49 loop : -1.42 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 353 HIS 0.007 0.002 HIS A 241 PHE 0.023 0.002 PHE A 28 TYR 0.028 0.002 TYR A 587 ARG 0.007 0.001 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 193 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 167 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 408 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7927 (ptm-80) REVERT: A 30 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: A 74 GLU cc_start: 0.7609 (tp30) cc_final: 0.7372 (tp30) REVERT: A 75 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7383 (tm-30) REVERT: A 190 MET cc_start: 0.7932 (tmm) cc_final: 0.7568 (ttt) REVERT: A 335 GLU cc_start: 0.7766 (tp30) cc_final: 0.7052 (mm-30) REVERT: A 340 ARG cc_start: 0.7939 (mtm-85) cc_final: 0.7584 (mtm-85) REVERT: A 341 LYS cc_start: 0.7912 (mttt) cc_final: 0.7619 (mttt) REVERT: A 455 MET cc_start: 0.8256 (tmm) cc_final: 0.7904 (tmm) REVERT: A 483 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7410 (tp30) REVERT: A 509 ASP cc_start: 0.7099 (p0) cc_final: 0.6777 (p0) REVERT: A 525 PHE cc_start: 0.8587 (m-10) cc_final: 0.8332 (m-10) REVERT: A 564 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: A 568 LEU cc_start: 0.8699 (tp) cc_final: 0.8499 (tp) REVERT: A 572 ASN cc_start: 0.8358 (m-40) cc_final: 0.8140 (m110) outliers start: 26 outliers final: 11 residues processed: 178 average time/residue: 1.1499 time to fit residues: 215.7722 Evaluate side-chains 182 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 167 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 171 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 483 GLU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 608 THR 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 42 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 30 optimal weight: 0.0970 chunk 63 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 0.0070 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6522 Z= 0.230 Angle : 0.568 7.656 8856 Z= 0.288 Chirality : 0.041 0.131 929 Planarity : 0.004 0.044 1144 Dihedral : 5.146 54.310 875 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.52 % Allowed : 21.00 % 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: 0.24 (0.31), residues: 776 helix: 1.25 (0.28), residues: 369 sheet: 2.07 (0.76), residues: 49 loop : -1.34 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 353 HIS 0.004 0.001 HIS A 241 PHE 0.019 0.001 PHE A 28 TYR 0.022 0.001 TYR A 183 ARG 0.007 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 192 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 168 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 350 VAL cc_start: 0.8296 (t) cc_final: 0.7974 (p) REVERT: A 30 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6949 (mp0) REVERT: A 74 GLU cc_start: 0.7580 (tp30) cc_final: 0.7189 (tp30) REVERT: A 75 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7429 (tm-30) REVERT: A 190 MET cc_start: 0.7928 (tmm) cc_final: 0.7510 (ttt) REVERT: A 206 ASP cc_start: 0.8175 (t0) cc_final: 0.7903 (t0) REVERT: A 335 GLU cc_start: 0.7843 (tp30) cc_final: 0.7315 (mm-30) REVERT: A 341 LYS cc_start: 0.7887 (mttt) cc_final: 0.7606 (mttt) REVERT: A 455 MET cc_start: 0.8220 (tmm) cc_final: 0.7999 (tmm) REVERT: A 483 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7365 (tp30) REVERT: A 509 ASP cc_start: 0.7021 (p0) cc_final: 0.6665 (p0) REVERT: A 541 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8297 (mttp) REVERT: A 568 LEU cc_start: 0.8690 (tp) cc_final: 0.8401 (tt) REVERT: A 572 ASN cc_start: 0.8348 (m-40) cc_final: 0.8003 (m110) outliers start: 24 outliers final: 14 residues processed: 178 average time/residue: 1.0681 time to fit residues: 200.3669 Evaluate side-chains 176 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 159 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 85 SER Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 334 THR 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 462 MET Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 608 THR 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 67 optimal weight: 0.0970 chunk 14 optimal weight: 0.0170 chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 34 optimal weight: 0.0980 chunk 6 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 0.2980 overall best weight: 0.2016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6522 Z= 0.165 Angle : 0.532 6.979 8856 Z= 0.266 Chirality : 0.040 0.127 929 Planarity : 0.004 0.043 1144 Dihedral : 4.883 58.446 875 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.08 % Allowed : 22.32 % 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: 0.46 (0.31), residues: 776 helix: 1.46 (0.28), residues: 366 sheet: 1.72 (0.76), residues: 51 loop : -1.18 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 353 HIS 0.003 0.001 HIS A 540 PHE 0.019 0.001 PHE A 28 TYR 0.023 0.001 TYR A 183 ARG 0.007 0.000 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 181 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 365 TYR cc_start: 0.8466 (m-10) cc_final: 0.8232 (m-10) REVERT: A 30 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6834 (mp0) REVERT: A 66 GLU cc_start: 0.7808 (tp30) cc_final: 0.7274 (tp30) REVERT: A 74 GLU cc_start: 0.7587 (tp30) cc_final: 0.7159 (tp30) REVERT: A 75 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7511 (tm-30) REVERT: A 190 MET cc_start: 0.7926 (tmm) cc_final: 0.7473 (ttt) REVERT: A 335 GLU cc_start: 0.7838 (tp30) cc_final: 0.7335 (mm-30) REVERT: A 341 LYS cc_start: 0.7898 (mttt) cc_final: 0.7644 (mttt) REVERT: A 483 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7328 (tp30) REVERT: A 509 ASP cc_start: 0.6950 (p0) cc_final: 0.6566 (p0) REVERT: A 541 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8303 (mttp) REVERT: A 568 LEU cc_start: 0.8680 (tp) cc_final: 0.8383 (tt) REVERT: A 572 ASN cc_start: 0.8329 (m-40) cc_final: 0.7996 (m110) outliers start: 21 outliers final: 13 residues processed: 168 average time/residue: 1.2419 time to fit residues: 220.1338 Evaluate side-chains 173 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 157 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain A residue 30 GLU 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 350 ASP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 608 THR 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 8 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 29 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 6522 Z= 0.406 Angle : 0.633 8.587 8856 Z= 0.326 Chirality : 0.046 0.134 929 Planarity : 0.005 0.045 1144 Dihedral : 5.167 55.990 875 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.67 % Allowed : 22.47 % Favored : 73.86 % 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 (0.31), residues: 776 helix: 1.17 (0.28), residues: 373 sheet: 1.64 (0.75), residues: 51 loop : -1.47 (0.31), residues: 352 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 0.022 0.002 PHE A 28 TYR 0.027 0.002 TYR A 587 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 186 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 161 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 350 VAL cc_start: 0.8343 (t) cc_final: 0.8073 (p) REVERT: B 408 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7948 (ptm-80) REVERT: A 30 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: A 66 GLU cc_start: 0.7883 (tp30) cc_final: 0.7301 (tp30) REVERT: A 74 GLU cc_start: 0.7619 (tp30) cc_final: 0.7390 (tp30) REVERT: A 75 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7402 (tm-30) REVERT: A 190 MET cc_start: 0.7965 (tmm) cc_final: 0.7580 (ttt) REVERT: A 335 GLU cc_start: 0.7821 (tp30) cc_final: 0.7350 (mm-30) REVERT: A 483 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7377 (tp30) REVERT: A 509 ASP cc_start: 0.7107 (p0) cc_final: 0.6751 (p0) REVERT: A 525 PHE cc_start: 0.8598 (m-10) cc_final: 0.8354 (m-10) REVERT: A 564 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: A 568 LEU cc_start: 0.8732 (tp) cc_final: 0.8510 (tp) outliers start: 25 outliers final: 15 residues processed: 170 average time/residue: 1.1631 time to fit residues: 208.7321 Evaluate side-chains 181 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 334 THR 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 483 GLU Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 608 THR 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 22 optimal weight: 0.9980 chunk 14 optimal weight: 0.0980 chunk 47 optimal weight: 0.5980 chunk 50 optimal weight: 0.0980 chunk 36 optimal weight: 0.3980 chunk 6 optimal weight: 0.4980 chunk 58 optimal weight: 0.0770 chunk 67 optimal weight: 0.5980 chunk 71 optimal weight: 0.1980 chunk 64 optimal weight: 0.2980 chunk 69 optimal weight: 0.5980 overall best weight: 0.1538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 572 ASN A 598 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6522 Z= 0.155 Angle : 0.538 7.809 8856 Z= 0.271 Chirality : 0.040 0.129 929 Planarity : 0.004 0.049 1144 Dihedral : 4.753 55.788 875 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.94 % Allowed : 22.32 % Favored : 74.74 % 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: 0.41 (0.31), residues: 776 helix: 1.45 (0.28), residues: 368 sheet: 1.92 (0.77), residues: 46 loop : -1.25 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 165 HIS 0.003 0.001 HIS A 378 PHE 0.019 0.001 PHE A 28 TYR 0.021 0.001 TYR A 183 ARG 0.006 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 182 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 365 TYR cc_start: 0.8447 (m-10) cc_final: 0.8224 (m-10) REVERT: A 30 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: A 66 GLU cc_start: 0.7816 (tp30) cc_final: 0.7472 (tp30) REVERT: A 74 GLU cc_start: 0.7593 (tp30) cc_final: 0.7201 (tp30) REVERT: A 75 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7521 (tm-30) REVERT: A 190 MET cc_start: 0.7903 (tmm) cc_final: 0.7446 (ttt) REVERT: A 206 ASP cc_start: 0.8156 (t0) cc_final: 0.7946 (t0) REVERT: A 335 GLU cc_start: 0.7845 (tp30) cc_final: 0.7418 (mm-30) REVERT: A 483 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7333 (tp30) REVERT: A 541 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8259 (mttp) REVERT: A 568 LEU cc_start: 0.8613 (tp) cc_final: 0.8395 (tt) outliers start: 20 outliers final: 11 residues processed: 169 average time/residue: 1.1304 time to fit residues: 200.9255 Evaluate side-chains 174 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 160 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 0.0970 chunk 65 optimal weight: 0.4980 chunk 68 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 572 ASN A 598 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6522 Z= 0.331 Angle : 0.621 9.383 8856 Z= 0.317 Chirality : 0.045 0.163 929 Planarity : 0.005 0.047 1144 Dihedral : 5.101 59.102 875 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.79 % Allowed : 23.79 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.26 (0.28), residues: 373 sheet: 1.72 (0.76), residues: 51 loop : -1.41 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 165 HIS 0.006 0.001 HIS A 241 PHE 0.023 0.002 PHE A 28 TYR 0.023 0.002 TYR A 587 ARG 0.008 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 181 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 408 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7961 (ptm-80) REVERT: A 30 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6992 (mp0) REVERT: A 66 GLU cc_start: 0.7876 (tp30) cc_final: 0.7537 (tp30) REVERT: A 74 GLU cc_start: 0.7596 (tp30) cc_final: 0.7156 (tp30) REVERT: A 75 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7420 (tm-30) REVERT: A 190 MET cc_start: 0.7946 (tmm) cc_final: 0.7530 (ttt) REVERT: A 335 GLU cc_start: 0.7823 (tp30) cc_final: 0.7259 (mm-30) REVERT: A 483 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7373 (tp30) REVERT: A 525 PHE cc_start: 0.8586 (m-10) cc_final: 0.8353 (m-10) REVERT: A 556 ASN cc_start: 0.8546 (t0) cc_final: 0.8321 (t0) REVERT: A 568 LEU cc_start: 0.8655 (tp) cc_final: 0.8404 (tt) outliers start: 19 outliers final: 16 residues processed: 170 average time/residue: 1.2139 time to fit residues: 217.8667 Evaluate side-chains 180 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 161 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 88 VAL 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 360 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 48 optimal weight: 0.0040 chunk 65 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 ASN A 175 GLN A 300 GLN A 572 ASN A 598 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6522 Z= 0.314 Angle : 0.635 9.350 8856 Z= 0.321 Chirality : 0.044 0.137 929 Planarity : 0.005 0.045 1144 Dihedral : 5.164 59.968 875 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.94 % Allowed : 23.35 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.30), residues: 776 helix: 1.14 (0.28), residues: 373 sheet: 1.73 (0.76), residues: 51 loop : -1.46 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 165 HIS 0.005 0.001 HIS A 241 PHE 0.027 0.002 PHE A 28 TYR 0.024 0.002 TYR A 183 ARG 0.008 0.001 ARG A 559 ********************** 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 180 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 160 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 350 VAL cc_start: 0.8228 (t) cc_final: 0.8012 (p) REVERT: B 365 TYR cc_start: 0.8437 (m-10) cc_final: 0.8199 (m-10) REVERT: B 408 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7952 (ptm-80) REVERT: A 30 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: A 66 GLU cc_start: 0.7885 (tp30) cc_final: 0.7465 (tp30) REVERT: A 74 GLU cc_start: 0.7598 (tp30) cc_final: 0.7154 (tp30) REVERT: A 75 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7428 (tm-30) REVERT: A 190 MET cc_start: 0.7946 (tmm) cc_final: 0.7554 (ttt) REVERT: A 335 GLU cc_start: 0.7827 (tp30) cc_final: 0.7275 (mm-30) REVERT: A 483 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7342 (tp30) REVERT: A 525 PHE cc_start: 0.8601 (m-10) cc_final: 0.8361 (m-10) REVERT: A 568 LEU cc_start: 0.8656 (tp) cc_final: 0.8442 (tt) outliers start: 20 outliers final: 17 residues processed: 168 average time/residue: 1.0884 time to fit residues: 192.5818 Evaluate side-chains 177 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 157 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 126 ILE 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 360 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 608 THR 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: 0.7980 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 61 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 7 optimal weight: 0.0010 chunk 11 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 300 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 = 0.3708 r_free = 0.3708 target = 0.119298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.108145 restraints weight = 9546.608| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.89 r_work: 0.3446 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6522 Z= 0.306 Angle : 0.616 9.204 8856 Z= 0.315 Chirality : 0.044 0.182 929 Planarity : 0.005 0.045 1144 Dihedral : 5.135 58.769 875 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.08 % Allowed : 24.38 % Favored : 72.54 % 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: 1.15 (0.28), residues: 373 sheet: 1.75 (0.75), residues: 51 loop : -1.47 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 165 HIS 0.006 0.001 HIS A 241 PHE 0.028 0.002 PHE A 28 TYR 0.024 0.002 TYR A 183 ARG 0.008 0.000 ARG A 559 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3855.45 seconds wall clock time: 69 minutes 20.17 seconds (4160.17 seconds total)