Starting phenix.real_space_refine on Thu Feb 13 17:28:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yf0_39206/02_2025/8yf0_39206.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yf0_39206/02_2025/8yf0_39206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yf0_39206/02_2025/8yf0_39206.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yf0_39206/02_2025/8yf0_39206.map" model { file = "/net/cci-nas-00/data/ceres_data/8yf0_39206/02_2025/8yf0_39206.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yf0_39206/02_2025/8yf0_39206.cif" } resolution = 3.49 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= -0.001 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 5989 2.51 5 N 1519 2.21 5 O 1603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9181 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4505 Classifications: {'peptide': 567} Link IDs: {'PTRANS': 13, 'TRANS': 553} Chain breaks: 1 Chain: "C" Number of atoms: 4676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4676 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 15, 'TRANS': 576} Chain breaks: 1 Time building chain proxies: 5.47, per 1000 atoms: 0.60 Number of scatterers: 9181 At special positions: 0 Unit cell: (117.432, 100.656, 129.548, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 1603 8.00 N 1519 7.00 C 5989 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 974.7 milliseconds 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 4 sheets defined 73.6% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'B' and resid 133 through 160 removed outlier: 4.287A pdb=" N GLY B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 188 removed outlier: 3.932A pdb=" N LEU B 174 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA B 175 " --> pdb=" O VAL B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 194 removed outlier: 3.892A pdb=" N GLU B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 200 through 230 removed outlier: 3.964A pdb=" N MET B 206 " --> pdb=" O SER B 202 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU B 209 " --> pdb=" O GLY B 205 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASP B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ARG B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 250 removed outlier: 3.621A pdb=" N ASN B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 270 removed outlier: 3.958A pdb=" N LEU B 259 " --> pdb=" O TYR B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 284 removed outlier: 3.543A pdb=" N ILE B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE B 283 " --> pdb=" O TYR B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 295 removed outlier: 3.578A pdb=" N HIS B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 315 removed outlier: 3.818A pdb=" N TRP B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 removed outlier: 3.628A pdb=" N SER B 321 " --> pdb=" O TYR B 318 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE B 322 " --> pdb=" O GLY B 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 318 through 322' Processing helix chain 'B' and resid 332 through 352 removed outlier: 3.580A pdb=" N LEU B 338 " --> pdb=" O ARG B 334 " (cutoff:3.500A) Proline residue: B 343 - end of helix Processing helix chain 'B' and resid 357 through 365 removed outlier: 3.908A pdb=" N PHE B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 385 removed outlier: 3.783A pdb=" N THR B 380 " --> pdb=" O GLN B 376 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASN B 381 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 403 Processing helix chain 'B' and resid 416 through 439 removed outlier: 3.566A pdb=" N GLY B 421 " --> pdb=" O TYR B 417 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 467 removed outlier: 4.126A pdb=" N PHE B 459 " --> pdb=" O PHE B 455 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N SER B 460 " --> pdb=" O THR B 456 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR B 461 " --> pdb=" O MET B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 482 removed outlier: 4.169A pdb=" N MET B 471 " --> pdb=" O TRP B 467 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER B 482 " --> pdb=" O VAL B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 622 removed outlier: 4.672A pdb=" N GLU B 592 " --> pdb=" O THR B 588 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N GLY B 593 " --> pdb=" O GLY B 589 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET B 596 " --> pdb=" O GLU B 592 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU B 609 " --> pdb=" O THR B 605 " (cutoff:3.500A) Proline residue: B 610 - end of helix removed outlier: 3.868A pdb=" N VAL B 614 " --> pdb=" O PRO B 610 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER B 615 " --> pdb=" O GLY B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 644 removed outlier: 4.307A pdb=" N ALA B 629 " --> pdb=" O LEU B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 677 Processing helix chain 'B' and resid 681 through 708 removed outlier: 3.833A pdb=" N ILE B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 160 Processing helix chain 'C' and resid 162 through 188 removed outlier: 3.586A pdb=" N TRP C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C 175 " --> pdb=" O VAL C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 Processing helix chain 'C' and resid 200 through 205 removed outlier: 4.297A pdb=" N GLY C 205 " --> pdb=" O SER C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 230 removed outlier: 4.181A pdb=" N VAL C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N TYR C 212 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG C 228 " --> pdb=" O GLY C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 252 removed outlier: 3.694A pdb=" N SER C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 271 removed outlier: 4.010A pdb=" N GLY C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 282 Processing helix chain 'C' and resid 288 through 295 Processing helix chain 'C' and resid 295 through 315 removed outlier: 4.413A pdb=" N PHE C 299 " --> pdb=" O TRP C 295 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY C 304 " --> pdb=" O TRP C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 340 Processing helix chain 'C' and resid 341 through 352 Processing helix chain 'C' and resid 357 through 365 removed outlier: 3.644A pdb=" N PHE C 361 " --> pdb=" O SER C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 385 removed outlier: 3.528A pdb=" N ALA C 370 " --> pdb=" O LYS C 366 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG C 383 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA C 384 " --> pdb=" O THR C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 400 removed outlier: 4.723A pdb=" N VAL C 391 " --> pdb=" O HIS C 387 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE C 392 " --> pdb=" O PRO C 388 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SER C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 439 removed outlier: 3.732A pdb=" N PHE C 439 " --> pdb=" O PHE C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 466 removed outlier: 3.689A pdb=" N GLY C 452 " --> pdb=" O LEU C 448 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE C 459 " --> pdb=" O PHE C 455 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N SER C 460 " --> pdb=" O THR C 456 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY C 463 " --> pdb=" O PHE C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 483 Processing helix chain 'C' and resid 590 through 622 Proline residue: C 610 - end of helix removed outlier: 4.030A pdb=" N ASP C 620 " --> pdb=" O ALA C 616 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS C 621 " --> pdb=" O LEU C 617 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE C 622 " --> pdb=" O LEU C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 644 Processing helix chain 'C' and resid 647 through 677 removed outlier: 4.041A pdb=" N VAL C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ALA C 668 " --> pdb=" O ALA C 664 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU C 669 " --> pdb=" O SER C 665 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP C 670 " --> pdb=" O TRP C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 678 through 707 removed outlier: 4.638A pdb=" N THR C 683 " --> pdb=" O SER C 679 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N THR C 684 " --> pdb=" O ASP C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 726 Processing sheet with id=AA1, first strand: chain 'B' and resid 485 through 487 removed outlier: 3.615A pdb=" N ILE B 505 " --> pdb=" O LYS B 485 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 521 through 526 removed outlier: 6.346A pdb=" N LYS B 522 " --> pdb=" O ASN B 543 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N PHE B 545 " --> pdb=" O LYS B 522 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL B 524 " --> pdb=" O PHE B 545 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 504 through 507 removed outlier: 5.965A pdb=" N GLN C 504 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N GLU C 527 " --> pdb=" O GLN C 504 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N HIS C 506 " --> pdb=" O GLU C 527 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 530 through 532 removed outlier: 5.780A pdb=" N PHE C 531 " --> pdb=" O ILE C 552 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 595 hydrogen bonds defined for protein. 1779 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: 2.71 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2844 1.34 - 1.46: 1917 1.46 - 1.58: 4563 1.58 - 1.70: 0 1.70 - 1.81: 112 Bond restraints: 9436 Sorted by residual: bond pdb=" N TYR B 152 " pdb=" CA TYR B 152 " ideal model delta sigma weight residual 1.459 1.425 0.034 1.17e-02 7.31e+03 8.26e+00 bond pdb=" CA TYR B 152 " pdb=" C TYR B 152 " ideal model delta sigma weight residual 1.524 1.498 0.026 1.24e-02 6.50e+03 4.54e+00 bond pdb=" C GLN B 151 " pdb=" N TYR B 152 " ideal model delta sigma weight residual 1.334 1.308 0.026 1.23e-02 6.61e+03 4.31e+00 bond pdb=" CG1 ILE B 210 " pdb=" CD1 ILE B 210 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.75e+00 bond pdb=" C THR C 456 " pdb=" O THR C 456 " ideal model delta sigma weight residual 1.236 1.220 0.017 1.26e-02 6.30e+03 1.76e+00 ... (remaining 9431 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 12519 1.82 - 3.63: 191 3.63 - 5.45: 46 5.45 - 7.26: 6 7.26 - 9.08: 2 Bond angle restraints: 12764 Sorted by residual: angle pdb=" N TYR B 152 " pdb=" CA TYR B 152 " pdb=" C TYR B 152 " ideal model delta sigma weight residual 110.97 107.08 3.89 1.09e+00 8.42e-01 1.27e+01 angle pdb=" CB MET B 634 " pdb=" CG MET B 634 " pdb=" SD MET B 634 " ideal model delta sigma weight residual 112.70 121.78 -9.08 3.00e+00 1.11e-01 9.15e+00 angle pdb=" C SER C 272 " pdb=" N ILE C 273 " pdb=" CA ILE C 273 " ideal model delta sigma weight residual 120.33 122.59 -2.26 8.00e-01 1.56e+00 8.00e+00 angle pdb=" C PHE B 640 " pdb=" N PHE B 641 " pdb=" CA PHE B 641 " ideal model delta sigma weight residual 121.14 116.23 4.91 1.75e+00 3.27e-01 7.86e+00 angle pdb=" C ASP B 586 " pdb=" CA ASP B 586 " pdb=" CB ASP B 586 " ideal model delta sigma weight residual 110.42 115.96 -5.54 1.99e+00 2.53e-01 7.74e+00 ... (remaining 12759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 4785 17.78 - 35.56: 486 35.56 - 53.35: 79 53.35 - 71.13: 22 71.13 - 88.91: 3 Dihedral angle restraints: 5375 sinusoidal: 2080 harmonic: 3295 Sorted by residual: dihedral pdb=" CA HIS C 292 " pdb=" C HIS C 292 " pdb=" N LEU C 293 " pdb=" CA LEU C 293 " ideal model delta harmonic sigma weight residual 180.00 163.63 16.37 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA TRP C 222 " pdb=" C TRP C 222 " pdb=" N GLY C 223 " pdb=" CA GLY C 223 " ideal model delta harmonic sigma weight residual 180.00 163.65 16.35 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA VAL C 189 " pdb=" C VAL C 189 " pdb=" N LEU C 190 " pdb=" CA LEU C 190 " ideal model delta harmonic sigma weight residual 180.00 163.75 16.25 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 5372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 938 0.036 - 0.072: 328 0.072 - 0.107: 82 0.107 - 0.143: 20 0.143 - 0.179: 3 Chirality restraints: 1371 Sorted by residual: chirality pdb=" CG LEU B 689 " pdb=" CB LEU B 689 " pdb=" CD1 LEU B 689 " pdb=" CD2 LEU B 689 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.00e-01 chirality pdb=" CG LEU B 603 " pdb=" CB LEU B 603 " pdb=" CD1 LEU B 603 " pdb=" CD2 LEU B 603 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" CB THR C 456 " pdb=" CA THR C 456 " pdb=" OG1 THR C 456 " pdb=" CG2 THR C 456 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 1368 not shown) Planarity restraints: 1606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 468 " -0.036 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO B 469 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 469 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 469 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 222 " 0.012 2.00e-02 2.50e+03 1.10e-02 3.02e+00 pdb=" CG TRP C 222 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP C 222 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP C 222 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 222 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 222 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 222 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 222 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 222 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 222 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 220 " 0.014 2.00e-02 2.50e+03 1.22e-02 2.60e+00 pdb=" CG PHE B 220 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE B 220 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 220 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 220 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 220 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 220 " 0.002 2.00e-02 2.50e+03 ... (remaining 1603 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2307 2.80 - 3.32: 9479 3.32 - 3.85: 15436 3.85 - 4.37: 17042 4.37 - 4.90: 29059 Nonbonded interactions: 73323 Sorted by model distance: nonbonded pdb=" O GLN B 253 " pdb=" OG1 THR B 257 " model vdw 2.271 3.040 nonbonded pdb=" OH TYR C 169 " pdb=" O TRP C 295 " model vdw 2.284 3.040 nonbonded pdb=" OH TYR B 279 " pdb=" O PRO B 355 " model vdw 2.289 3.040 nonbonded pdb=" O TYR B 443 " pdb=" OG1 THR B 447 " model vdw 2.290 3.040 nonbonded pdb=" OD2 ASP B 196 " pdb=" NE1 TRP B 333 " model vdw 2.295 3.120 ... (remaining 73318 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 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'C' and resid 133 through 709) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 22.800 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 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 0.065 9436 Z= 0.192 Angle : 0.593 9.075 12764 Z= 0.314 Chirality : 0.040 0.179 1371 Planarity : 0.003 0.054 1606 Dihedral : 14.647 88.910 3275 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: 0.97 (0.25), residues: 1151 helix: 1.23 (0.19), residues: 770 sheet: -0.36 (1.84), residues: 10 loop : -0.46 (0.35), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 222 HIS 0.005 0.001 HIS C 378 PHE 0.028 0.001 PHE B 220 TYR 0.018 0.001 TYR B 306 ARG 0.009 0.000 ARG C 157 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: B 298 MET cc_start: 0.5694 (mmp) cc_final: 0.5417 (mmp) REVERT: B 454 TRP cc_start: 0.5900 (m100) cc_final: 0.5261 (m-10) REVERT: B 470 ASP cc_start: 0.8060 (m-30) cc_final: 0.7800 (m-30) REVERT: B 596 MET cc_start: 0.7095 (ppp) cc_final: 0.6822 (ppp) REVERT: C 324 MET cc_start: 0.2572 (mtp) cc_final: 0.2284 (mtp) REVERT: C 457 MET cc_start: 0.6210 (tmm) cc_final: 0.5987 (tmm) REVERT: C 464 LEU cc_start: 0.7313 (mm) cc_final: 0.7049 (mm) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1793 time to fit residues: 44.8474 Evaluate side-chains 148 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 30.0000 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5034 r_free = 0.5034 target = 0.261771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.214604 restraints weight = 13807.565| |-----------------------------------------------------------------------------| r_work (start): 0.4588 rms_B_bonded: 4.12 r_work: 0.4264 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9436 Z= 0.360 Angle : 0.713 11.573 12764 Z= 0.368 Chirality : 0.043 0.156 1371 Planarity : 0.005 0.068 1606 Dihedral : 4.486 20.919 1253 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.03 % Allowed : 10.50 % Favored : 88.47 % 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: 0.40 (0.24), residues: 1151 helix: 0.77 (0.18), residues: 765 sheet: -0.12 (1.89), residues: 10 loop : -0.60 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 222 HIS 0.007 0.001 HIS C 292 PHE 0.024 0.002 PHE B 644 TYR 0.031 0.002 TYR B 462 ARG 0.005 0.001 ARG B 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: B 152 TYR cc_start: 0.7524 (t80) cc_final: 0.7210 (t80) REVERT: B 216 MET cc_start: 0.6840 (ptp) cc_final: 0.6502 (ptp) REVERT: B 298 MET cc_start: 0.6225 (mmp) cc_final: 0.5850 (mmp) REVERT: B 312 TRP cc_start: 0.7003 (t60) cc_final: 0.6520 (t60) REVERT: C 184 PHE cc_start: 0.7897 (t80) cc_final: 0.7668 (t80) REVERT: C 317 HIS cc_start: 0.7201 (t70) cc_final: 0.6872 (t70) REVERT: C 324 MET cc_start: 0.3000 (mtp) cc_final: 0.2695 (mtp) REVERT: C 464 LEU cc_start: 0.7836 (mm) cc_final: 0.7509 (mm) REVERT: C 599 PHE cc_start: 0.7513 (OUTLIER) cc_final: 0.7288 (t80) outliers start: 10 outliers final: 7 residues processed: 147 average time/residue: 0.1949 time to fit residues: 41.1694 Evaluate side-chains 140 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 599 PHE Chi-restraints excluded: chain C residue 636 CYS Chi-restraints excluded: chain C residue 655 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 28 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 61 optimal weight: 0.1980 chunk 49 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 82 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 91 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 233 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5075 r_free = 0.5075 target = 0.267160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.210121 restraints weight = 13925.948| |-----------------------------------------------------------------------------| r_work (start): 0.4557 rms_B_bonded: 3.60 r_work: 0.4357 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9436 Z= 0.166 Angle : 0.579 11.490 12764 Z= 0.296 Chirality : 0.039 0.149 1371 Planarity : 0.004 0.065 1606 Dihedral : 4.269 20.320 1253 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.93 % Allowed : 14.93 % Favored : 84.14 % 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: 0.88 (0.25), residues: 1151 helix: 1.18 (0.18), residues: 769 sheet: -0.07 (1.91), residues: 10 loop : -0.54 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 222 HIS 0.004 0.001 HIS C 292 PHE 0.023 0.001 PHE B 640 TYR 0.029 0.001 TYR B 169 ARG 0.004 0.000 ARG C 157 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: B 152 TYR cc_start: 0.7574 (t80) cc_final: 0.7228 (t80) REVERT: B 212 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.6800 (t80) REVERT: B 216 MET cc_start: 0.6649 (ptp) cc_final: 0.6299 (ptp) REVERT: B 298 MET cc_start: 0.6048 (mmp) cc_final: 0.5610 (mmp) REVERT: C 317 HIS cc_start: 0.7162 (t70) cc_final: 0.6844 (t70) REVERT: C 324 MET cc_start: 0.2767 (mtp) cc_final: 0.2473 (mtp) REVERT: C 464 LEU cc_start: 0.7756 (mm) cc_final: 0.7329 (mm) outliers start: 9 outliers final: 5 residues processed: 155 average time/residue: 0.2015 time to fit residues: 46.1694 Evaluate side-chains 151 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 145 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 655 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 24 optimal weight: 6.9990 chunk 113 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 44 optimal weight: 0.0570 chunk 84 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5144 r_free = 0.5144 target = 0.270325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.222541 restraints weight = 13691.809| |-----------------------------------------------------------------------------| r_work (start): 0.4722 rms_B_bonded: 3.04 r_work: 0.4519 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9436 Z= 0.167 Angle : 0.560 10.476 12764 Z= 0.288 Chirality : 0.039 0.132 1371 Planarity : 0.004 0.066 1606 Dihedral : 4.151 19.706 1253 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.85 % Allowed : 16.07 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.25), residues: 1151 helix: 1.35 (0.18), residues: 771 sheet: -0.09 (1.89), residues: 10 loop : -0.49 (0.35), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 222 HIS 0.003 0.001 HIS C 292 PHE 0.023 0.001 PHE B 435 TYR 0.026 0.001 TYR B 169 ARG 0.005 0.000 ARG C 157 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: B 152 TYR cc_start: 0.7250 (t80) cc_final: 0.6968 (t80) REVERT: B 212 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.6799 (t80) REVERT: B 216 MET cc_start: 0.6612 (ptp) cc_final: 0.6369 (ptp) REVERT: B 298 MET cc_start: 0.6193 (mmp) cc_final: 0.5724 (mmp) REVERT: B 663 ILE cc_start: 0.7722 (mt) cc_final: 0.7398 (mt) REVERT: C 148 LEU cc_start: 0.8604 (mm) cc_final: 0.8255 (pp) REVERT: C 317 HIS cc_start: 0.6944 (t70) cc_final: 0.6642 (t70) REVERT: C 324 MET cc_start: 0.2721 (mtp) cc_final: 0.2436 (mtp) REVERT: C 464 LEU cc_start: 0.7549 (mm) cc_final: 0.7120 (mm) outliers start: 18 outliers final: 9 residues processed: 167 average time/residue: 0.1873 time to fit residues: 45.0080 Evaluate side-chains 156 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 596 MET Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 655 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 42 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 78 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 396 HIS ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5108 r_free = 0.5108 target = 0.265404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.218790 restraints weight = 13669.614| |-----------------------------------------------------------------------------| r_work (start): 0.4684 rms_B_bonded: 3.68 r_work: 0.4410 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.4410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9436 Z= 0.292 Angle : 0.658 11.970 12764 Z= 0.338 Chirality : 0.041 0.147 1371 Planarity : 0.004 0.067 1606 Dihedral : 4.338 20.652 1253 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.27 % Allowed : 17.82 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1151 helix: 0.97 (0.18), residues: 768 sheet: -0.11 (1.90), residues: 10 loop : -0.57 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 222 HIS 0.007 0.001 HIS C 292 PHE 0.020 0.002 PHE B 184 TYR 0.029 0.002 TYR B 169 ARG 0.005 0.000 ARG C 157 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 152 TYR cc_start: 0.7364 (t80) cc_final: 0.7069 (t80) REVERT: B 212 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.6989 (t80) REVERT: B 216 MET cc_start: 0.6803 (ptp) cc_final: 0.6594 (ptp) REVERT: B 261 CYS cc_start: 0.6624 (OUTLIER) cc_final: 0.6332 (t) REVERT: B 295 TRP cc_start: 0.7525 (m100) cc_final: 0.7168 (m100) REVERT: B 298 MET cc_start: 0.5915 (mmp) cc_final: 0.5491 (mmp) REVERT: C 317 HIS cc_start: 0.7197 (t70) cc_final: 0.6907 (t70) REVERT: C 324 MET cc_start: 0.2771 (mtp) cc_final: 0.2519 (mtp) REVERT: C 364 ASN cc_start: 0.6760 (p0) cc_final: 0.6542 (p0) REVERT: C 464 LEU cc_start: 0.7766 (mm) cc_final: 0.7377 (mm) outliers start: 22 outliers final: 15 residues processed: 156 average time/residue: 0.1954 time to fit residues: 43.7673 Evaluate side-chains 151 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 596 MET Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 655 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 3 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 396 HIS B 476 GLN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5116 r_free = 0.5116 target = 0.266268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.219920 restraints weight = 13564.870| |-----------------------------------------------------------------------------| r_work (start): 0.4691 rms_B_bonded: 3.51 r_work: 0.4431 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 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 0.050 9436 Z= 0.258 Angle : 0.647 12.724 12764 Z= 0.330 Chirality : 0.041 0.165 1371 Planarity : 0.004 0.068 1606 Dihedral : 4.354 20.540 1253 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.16 % Allowed : 18.95 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.62 (0.25), residues: 1151 helix: 0.94 (0.18), residues: 769 sheet: -0.12 (1.90), residues: 10 loop : -0.55 (0.35), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 222 HIS 0.005 0.001 HIS C 292 PHE 0.024 0.002 PHE B 184 TYR 0.030 0.002 TYR B 169 ARG 0.006 0.000 ARG C 157 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 152 TYR cc_start: 0.7344 (t80) cc_final: 0.7046 (t80) REVERT: B 206 MET cc_start: 0.6348 (tpt) cc_final: 0.6011 (tpt) REVERT: B 212 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.6966 (t80) REVERT: B 261 CYS cc_start: 0.6531 (OUTLIER) cc_final: 0.6237 (t) REVERT: C 148 LEU cc_start: 0.8722 (mm) cc_final: 0.8362 (pp) REVERT: C 317 HIS cc_start: 0.6933 (t70) cc_final: 0.6663 (t70) REVERT: C 324 MET cc_start: 0.2706 (mtp) cc_final: 0.2456 (mtp) REVERT: C 364 ASN cc_start: 0.6724 (p0) cc_final: 0.6507 (p0) REVERT: C 464 LEU cc_start: 0.7705 (mm) cc_final: 0.7263 (mm) REVERT: C 599 PHE cc_start: 0.7280 (OUTLIER) cc_final: 0.6796 (t80) outliers start: 21 outliers final: 15 residues processed: 157 average time/residue: 0.2074 time to fit residues: 46.3408 Evaluate side-chains 155 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 596 MET Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 599 PHE Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 655 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 46 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 chunk 63 optimal weight: 0.5980 chunk 75 optimal weight: 0.0050 chunk 90 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 396 HIS ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5136 r_free = 0.5136 target = 0.269331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.222206 restraints weight = 13686.853| |-----------------------------------------------------------------------------| r_work (start): 0.4718 rms_B_bonded: 3.21 r_work: 0.4491 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.4491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9436 Z= 0.183 Angle : 0.612 11.771 12764 Z= 0.310 Chirality : 0.039 0.142 1371 Planarity : 0.004 0.066 1606 Dihedral : 4.193 19.225 1253 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.16 % Allowed : 19.57 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.25), residues: 1151 helix: 1.23 (0.18), residues: 770 sheet: -0.11 (1.89), residues: 10 loop : -0.51 (0.35), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 222 HIS 0.010 0.001 HIS B 396 PHE 0.032 0.001 PHE B 184 TYR 0.029 0.001 TYR B 169 ARG 0.007 0.000 ARG C 157 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 152 TYR cc_start: 0.7254 (t80) cc_final: 0.7012 (t80) REVERT: B 206 MET cc_start: 0.6359 (tpt) cc_final: 0.5976 (tpt) REVERT: B 212 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.6953 (t80) REVERT: B 261 CYS cc_start: 0.6456 (OUTLIER) cc_final: 0.6179 (t) REVERT: B 295 TRP cc_start: 0.7542 (m100) cc_final: 0.7327 (m100) REVERT: B 468 PHE cc_start: 0.6802 (p90) cc_final: 0.6279 (p90) REVERT: C 148 LEU cc_start: 0.8681 (mm) cc_final: 0.8342 (pp) REVERT: C 317 HIS cc_start: 0.6876 (t70) cc_final: 0.6600 (t70) REVERT: C 324 MET cc_start: 0.2533 (mtp) cc_final: 0.2316 (mtp) REVERT: C 364 ASN cc_start: 0.6667 (p0) cc_final: 0.6460 (p0) REVERT: C 464 LEU cc_start: 0.7624 (mm) cc_final: 0.7155 (mm) REVERT: C 599 PHE cc_start: 0.7157 (OUTLIER) cc_final: 0.6739 (t80) outliers start: 21 outliers final: 12 residues processed: 161 average time/residue: 0.1979 time to fit residues: 45.7651 Evaluate side-chains 159 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 596 MET Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 599 PHE Chi-restraints excluded: chain C residue 655 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 84 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 80 optimal weight: 0.1980 chunk 100 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5134 r_free = 0.5134 target = 0.269042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.223463 restraints weight = 13753.567| |-----------------------------------------------------------------------------| r_work (start): 0.4731 rms_B_bonded: 3.49 r_work: 0.4480 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9436 Z= 0.192 Angle : 0.620 11.106 12764 Z= 0.315 Chirality : 0.039 0.150 1371 Planarity : 0.004 0.066 1606 Dihedral : 4.152 18.752 1253 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.06 % Allowed : 20.19 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.25), residues: 1151 helix: 1.29 (0.18), residues: 770 sheet: -0.15 (1.88), residues: 10 loop : -0.50 (0.35), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 222 HIS 0.005 0.001 HIS C 378 PHE 0.033 0.001 PHE B 184 TYR 0.029 0.001 TYR B 169 ARG 0.008 0.000 ARG C 157 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 152 TYR cc_start: 0.7274 (t80) cc_final: 0.7057 (t80) REVERT: B 206 MET cc_start: 0.6349 (tpt) cc_final: 0.5966 (tpt) REVERT: B 212 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.7013 (t80) REVERT: B 261 CYS cc_start: 0.6449 (OUTLIER) cc_final: 0.6180 (t) REVERT: B 295 TRP cc_start: 0.7514 (m100) cc_final: 0.7180 (m100) REVERT: B 298 MET cc_start: 0.6099 (mmp) cc_final: 0.5203 (mmp) REVERT: B 666 TRP cc_start: 0.7296 (m100) cc_final: 0.7094 (m100) REVERT: C 148 LEU cc_start: 0.8696 (mm) cc_final: 0.8368 (pp) REVERT: C 317 HIS cc_start: 0.6979 (t70) cc_final: 0.6684 (t70) REVERT: C 324 MET cc_start: 0.2506 (mtp) cc_final: 0.2287 (mtp) REVERT: C 464 LEU cc_start: 0.7667 (mm) cc_final: 0.7184 (mm) REVERT: C 599 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6840 (t80) outliers start: 20 outliers final: 16 residues processed: 158 average time/residue: 0.1967 time to fit residues: 44.9370 Evaluate side-chains 161 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 596 MET Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 599 PHE Chi-restraints excluded: chain C residue 636 CYS Chi-restraints excluded: chain C residue 655 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 106 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5120 r_free = 0.5120 target = 0.267534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.222740 restraints weight = 13056.986| |-----------------------------------------------------------------------------| r_work (start): 0.4734 rms_B_bonded: 3.48 r_work: 0.4482 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.4482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9436 Z= 0.198 Angle : 0.626 10.824 12764 Z= 0.318 Chirality : 0.039 0.156 1371 Planarity : 0.004 0.066 1606 Dihedral : 4.139 18.382 1253 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.37 % Allowed : 20.60 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.25), residues: 1151 helix: 1.30 (0.18), residues: 771 sheet: -0.14 (1.87), residues: 10 loop : -0.49 (0.35), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 222 HIS 0.017 0.001 HIS B 396 PHE 0.032 0.001 PHE B 184 TYR 0.030 0.001 TYR B 169 ARG 0.010 0.000 ARG C 157 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 206 MET cc_start: 0.6343 (tpt) cc_final: 0.5958 (tpt) REVERT: B 212 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.7021 (t80) REVERT: B 261 CYS cc_start: 0.6454 (OUTLIER) cc_final: 0.6192 (t) REVERT: B 295 TRP cc_start: 0.7570 (m100) cc_final: 0.7229 (m100) REVERT: B 298 MET cc_start: 0.6115 (mmp) cc_final: 0.5234 (mmp) REVERT: C 148 LEU cc_start: 0.8667 (mm) cc_final: 0.8358 (pp) REVERT: C 227 ASP cc_start: 0.6830 (OUTLIER) cc_final: 0.6557 (t0) REVERT: C 317 HIS cc_start: 0.6963 (t70) cc_final: 0.6669 (t70) REVERT: C 324 MET cc_start: 0.2556 (mtp) cc_final: 0.2329 (mtp) REVERT: C 464 LEU cc_start: 0.7696 (mm) cc_final: 0.7217 (mm) REVERT: C 599 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.6825 (t80) outliers start: 23 outliers final: 16 residues processed: 159 average time/residue: 0.1999 time to fit residues: 45.9483 Evaluate side-chains 162 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 596 MET Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 599 PHE Chi-restraints excluded: chain C residue 636 CYS Chi-restraints excluded: chain C residue 655 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 38 optimal weight: 30.0000 chunk 96 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 chunk 114 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5124 r_free = 0.5124 target = 0.267438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.223049 restraints weight = 13255.391| |-----------------------------------------------------------------------------| r_work (start): 0.4734 rms_B_bonded: 3.67 r_work: 0.4465 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.4465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9436 Z= 0.217 Angle : 0.656 14.114 12764 Z= 0.333 Chirality : 0.040 0.157 1371 Planarity : 0.004 0.066 1606 Dihedral : 4.173 18.339 1253 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.16 % Allowed : 21.52 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.25), residues: 1151 helix: 1.27 (0.18), residues: 771 sheet: -0.15 (1.87), residues: 10 loop : -0.49 (0.35), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 222 HIS 0.016 0.001 HIS B 396 PHE 0.029 0.001 PHE B 184 TYR 0.029 0.002 TYR B 169 ARG 0.010 0.000 ARG C 157 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 206 MET cc_start: 0.6352 (tpt) cc_final: 0.5956 (tpt) REVERT: B 212 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.7032 (t80) REVERT: B 261 CYS cc_start: 0.6483 (OUTLIER) cc_final: 0.6210 (t) REVERT: B 454 TRP cc_start: 0.6416 (m100) cc_final: 0.5698 (m-10) REVERT: B 666 TRP cc_start: 0.7335 (m100) cc_final: 0.7052 (m100) REVERT: C 148 LEU cc_start: 0.8716 (mm) cc_final: 0.8388 (pp) REVERT: C 227 ASP cc_start: 0.6837 (OUTLIER) cc_final: 0.6561 (t0) REVERT: C 317 HIS cc_start: 0.7025 (t70) cc_final: 0.6698 (t70) REVERT: C 324 MET cc_start: 0.2604 (mtp) cc_final: 0.2360 (mtp) REVERT: C 464 LEU cc_start: 0.7717 (mm) cc_final: 0.7246 (mm) REVERT: C 599 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.6961 (t80) REVERT: C 603 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7588 (mm) REVERT: C 658 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7662 (t80) REVERT: C 704 PHE cc_start: 0.6045 (m-10) cc_final: 0.5683 (m-10) outliers start: 21 outliers final: 14 residues processed: 155 average time/residue: 0.1946 time to fit residues: 43.1360 Evaluate side-chains 158 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 596 MET Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 599 PHE Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 636 CYS Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 658 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 1.9990 chunk 70 optimal weight: 0.0980 chunk 8 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 41 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5145 r_free = 0.5145 target = 0.270493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.225051 restraints weight = 13713.315| |-----------------------------------------------------------------------------| r_work (start): 0.4746 rms_B_bonded: 3.51 r_work: 0.4492 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.4492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9436 Z= 0.185 Angle : 0.645 13.382 12764 Z= 0.326 Chirality : 0.040 0.193 1371 Planarity : 0.004 0.066 1606 Dihedral : 4.108 17.482 1253 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.16 % Allowed : 21.01 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.25), residues: 1151 helix: 1.39 (0.18), residues: 771 sheet: -0.17 (1.86), residues: 10 loop : -0.46 (0.35), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 222 HIS 0.016 0.001 HIS B 396 PHE 0.028 0.001 PHE B 184 TYR 0.031 0.001 TYR B 169 ARG 0.010 0.000 ARG C 157 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5208.60 seconds wall clock time: 92 minutes 47.30 seconds (5567.30 seconds total)