Starting phenix.real_space_refine on Thu Mar 5 11:54:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fpf_29362/03_2026/8fpf_29362_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fpf_29362/03_2026/8fpf_29362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fpf_29362/03_2026/8fpf_29362_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fpf_29362/03_2026/8fpf_29362_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fpf_29362/03_2026/8fpf_29362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fpf_29362/03_2026/8fpf_29362.map" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.027 sd= 0.067 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: 6 Type Number sf(0) Gaussians P 21 5.49 5 S 39 5.16 5 C 6982 2.51 5 N 1659 2.21 5 O 1923 1.98 5 H 9854 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20478 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 10708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 10708 Classifications: {'peptide': 666} Link IDs: {'PTRANS': 13, 'TRANS': 652} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 8861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 8861 Classifications: {'peptide': 558} Link IDs: {'PTRANS': 19, 'TRANS': 538} Chain breaks: 1 Chain: "D" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 493 Unusual residues: {'ATP': 1, 'POV': 14} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 331 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 5, 'POV:plan-3': 6} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 416 Unusual residues: {'ATP': 1, 'POV': 11} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-1': 4, 'POV:plan-2': 3, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 25 Time building chain proxies: 3.47, per 1000 atoms: 0.17 Number of scatterers: 20478 At special positions: 0 Unit cell: (75.9, 105.6, 159.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 39 16.00 P 21 15.00 O 1923 8.00 N 1659 7.00 C 6982 6.00 H 9854 1.00 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: 2.44 Conformation dependent library (CDL) restraints added in 630.6 milliseconds 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2270 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 65.8% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'D' and resid 2 through 13 removed outlier: 3.669A pdb=" N LEU D 13 " --> pdb=" O ARG D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 48 removed outlier: 3.507A pdb=" N LEU D 18 " --> pdb=" O TYR D 14 " (cutoff:3.500A) Proline residue: D 36 - end of helix removed outlier: 3.721A pdb=" N HIS D 46 " --> pdb=" O MET D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 52 Processing helix chain 'D' and resid 136 through 143 Processing helix chain 'D' and resid 145 through 194 removed outlier: 3.768A pdb=" N PHE D 165 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE D 166 " --> pdb=" O PHE D 162 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR D 168 " --> pdb=" O VAL D 164 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'D' and resid 197 through 203 removed outlier: 4.096A pdb=" N PHE D 201 " --> pdb=" O PRO D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 249 removed outlier: 3.897A pdb=" N VAL D 209 " --> pdb=" O PRO D 205 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP D 216 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR D 217 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR D 233 " --> pdb=" O SER D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 removed outlier: 3.809A pdb=" N VAL D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 297 removed outlier: 4.201A pdb=" N TYR D 276 " --> pdb=" O ARG D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 305 Processing helix chain 'D' and resid 307 through 334 Processing helix chain 'D' and resid 338 through 363 removed outlier: 3.736A pdb=" N ALA D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 383 removed outlier: 3.525A pdb=" N LEU D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 411 removed outlier: 5.123A pdb=" N GLU D 397 " --> pdb=" O PHE D 393 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU D 398 " --> pdb=" O SER D 394 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 477 removed outlier: 3.997A pdb=" N LEU D 473 " --> pdb=" O LYS D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 497 No H-bonds generated for 'chain 'D' and resid 495 through 497' Processing helix chain 'D' and resid 498 through 505 removed outlier: 3.529A pdb=" N HIS D 505 " --> pdb=" O GLU D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 526 Processing helix chain 'D' and resid 534 through 536 No H-bonds generated for 'chain 'D' and resid 534 through 536' Processing helix chain 'D' and resid 537 through 542 removed outlier: 3.778A pdb=" N ARG D 541 " --> pdb=" O LYS D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 550 removed outlier: 4.119A pdb=" N LYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 563 removed outlier: 4.332A pdb=" N GLU D 562 " --> pdb=" O PRO D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 584 Processing helix chain 'D' and resid 601 through 614 removed outlier: 4.298A pdb=" N ILE D 605 " --> pdb=" O THR D 601 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN D 614 " --> pdb=" O ASP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 652 Processing helix chain 'D' and resid 655 through 666 removed outlier: 4.167A pdb=" N LYS D 666 " --> pdb=" O TYR D 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 8 through 15 removed outlier: 3.526A pdb=" N PHE C 12 " --> pdb=" O LEU C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 34 Processing helix chain 'C' and resid 35 through 49 removed outlier: 3.729A pdb=" N ALA C 49 " --> pdb=" O ASP C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 103 Processing helix chain 'C' and resid 105 through 112 removed outlier: 3.653A pdb=" N TYR C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 123 Processing helix chain 'C' and resid 123 through 157 removed outlier: 4.357A pdb=" N ILE C 136 " --> pdb=" O THR C 132 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N MET C 146 " --> pdb=" O SER C 142 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET C 147 " --> pdb=" O THR C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 166 Processing helix chain 'C' and resid 167 through 207 removed outlier: 4.346A pdb=" N VAL C 171 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU C 202 " --> pdb=" O ASN C 198 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU C 203 " --> pdb=" O ASP C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 removed outlier: 3.514A pdb=" N ILE C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 243 removed outlier: 3.878A pdb=" N ILE C 241 " --> pdb=" O LYS C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 271 removed outlier: 3.735A pdb=" N THR C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 289 Processing helix chain 'C' and resid 289 through 318 removed outlier: 4.376A pdb=" N PHE C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU C 314 " --> pdb=" O ASP C 310 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 383 Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 427 through 437 removed outlier: 4.650A pdb=" N GLY C 435 " --> pdb=" O ASN C 431 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS C 436 " --> pdb=" O ILE C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 451 removed outlier: 4.336A pdb=" N GLN C 445 " --> pdb=" O ASP C 441 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN C 446 " --> pdb=" O LYS C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 459 Processing helix chain 'C' and resid 478 through 491 removed outlier: 4.005A pdb=" N ALA C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 521 Processing helix chain 'C' and resid 533 through 537 removed outlier: 3.625A pdb=" N VAL C 536 " --> pdb=" O LEU C 533 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU C 537 " --> pdb=" O SER C 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 533 through 537' Processing helix chain 'C' and resid 555 through 561 Processing sheet with id=AA1, first strand: chain 'D' and resid 54 through 57 removed outlier: 4.336A pdb=" N SER D 71 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 89 through 93 Processing sheet with id=AA3, first strand: chain 'D' and resid 110 through 112 removed outlier: 3.891A pdb=" N ILE D 119 " --> pdb=" O ARG D 126 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG D 126 " --> pdb=" O ILE D 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 452 through 453 removed outlier: 4.080A pdb=" N VAL D 430 " --> pdb=" O ALA D 453 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 435 through 438 removed outlier: 7.662A pdb=" N PHE D 437 " --> pdb=" O LYS D 447 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LYS D 447 " --> pdb=" O PHE D 437 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 506 through 509 removed outlier: 6.499A pdb=" N GLY D 507 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ASP D 591 " --> pdb=" O GLY D 507 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL D 509 " --> pdb=" O ASP D 591 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU D 588 " --> pdb=" O PHE D 619 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ILE D 621 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU D 590 " --> pdb=" O ILE D 621 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 634 through 638 removed outlier: 7.105A pdb=" N ILE D 634 " --> pdb=" O ARG D 645 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ARG D 645 " --> pdb=" O ILE D 634 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL D 636 " --> pdb=" O VAL D 643 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 337 through 342 removed outlier: 5.127A pdb=" N ILE C 357 " --> pdb=" O HIS C 341 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 414 through 417 removed outlier: 5.993A pdb=" N GLY C 415 " --> pdb=" O ILE C 497 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ASP C 499 " --> pdb=" O GLY C 415 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL C 417 " --> pdb=" O ASP C 499 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU C 496 " --> pdb=" O PHE C 527 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LEU C 529 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU C 498 " --> pdb=" O LEU C 529 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR C 366 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LEU C 543 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLY C 368 " --> pdb=" O LEU C 543 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N MET C 545 " --> pdb=" O GLY C 368 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA C 370 " --> pdb=" O MET C 545 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU C 552 " --> pdb=" O VAL C 544 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASP C 546 " --> pdb=" O ILE C 550 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE C 550 " --> pdb=" O ASP C 546 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 396 through 397 removed outlier: 3.688A pdb=" N VAL C 400 " --> pdb=" O PHE C 397 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1755 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: 4.68 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 3240 1.05 - 1.24: 7891 1.24 - 1.43: 3002 1.43 - 1.62: 6433 1.62 - 1.81: 78 Bond restraints: 20644 Sorted by residual: bond pdb=" NE1 TRP D 8 " pdb=" HE1 TRP D 8 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP D 264 " pdb=" HE1 TRP D 264 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP C 78 " pdb=" HE1 TRP C 78 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP D 54 " pdb=" HE1 TRP D 54 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" NE1 TRP C 565 " pdb=" HE1 TRP C 565 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 ... (remaining 20639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.52: 36426 3.52 - 7.04: 297 7.04 - 10.56: 23 10.56 - 14.07: 1 14.07 - 17.59: 1 Bond angle restraints: 36748 Sorted by residual: angle pdb=" PB ATP C 612 " pdb=" O3B ATP C 612 " pdb=" PG ATP C 612 " ideal model delta sigma weight residual 139.87 122.28 17.59 1.00e+00 1.00e+00 3.09e+02 angle pdb=" PB ATP D 715 " pdb=" O3B ATP D 715 " pdb=" PG ATP D 715 " ideal model delta sigma weight residual 139.87 128.91 10.96 1.00e+00 1.00e+00 1.20e+02 angle pdb=" PA ATP C 612 " pdb=" O3A ATP C 612 " pdb=" PB ATP C 612 " ideal model delta sigma weight residual 136.83 127.46 9.37 1.00e+00 1.00e+00 8.77e+01 angle pdb=" PA ATP D 715 " pdb=" O3A ATP D 715 " pdb=" PB ATP D 715 " ideal model delta sigma weight residual 136.83 128.64 8.19 1.00e+00 1.00e+00 6.70e+01 angle pdb=" N LEU D 257 " pdb=" CA LEU D 257 " pdb=" C LEU D 257 " ideal model delta sigma weight residual 112.89 104.47 8.42 1.24e+00 6.50e-01 4.61e+01 ... (remaining 36743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 9527 35.31 - 70.63: 350 70.63 - 105.94: 45 105.94 - 141.25: 24 141.25 - 176.56: 4 Dihedral angle restraints: 9950 sinusoidal: 5737 harmonic: 4213 Sorted by residual: dihedral pdb=" C27 POV C 609 " pdb=" C28 POV C 609 " pdb=" C29 POV C 609 " pdb="C210 POV C 609 " ideal model delta sinusoidal sigma weight residual 127.48 -49.08 176.56 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C29 POV D 704 " pdb="C210 POV D 704 " pdb="C211 POV D 704 " pdb="C212 POV D 704 " ideal model delta sinusoidal sigma weight residual 112.25 -57.35 169.60 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C27 POV D 707 " pdb=" C28 POV D 707 " pdb=" C29 POV D 707 " pdb="C210 POV D 707 " ideal model delta sinusoidal sigma weight residual 127.48 -64.65 -167.87 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 9947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1075 0.037 - 0.074: 319 0.074 - 0.111: 99 0.111 - 0.147: 38 0.147 - 0.184: 12 Chirality restraints: 1543 Sorted by residual: chirality pdb=" CB ILE C 369 " pdb=" CA ILE C 369 " pdb=" CG1 ILE C 369 " pdb=" CG2 ILE C 369 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" CA ILE D 642 " pdb=" N ILE D 642 " pdb=" C ILE D 642 " pdb=" CB ILE D 642 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CA LEU C 529 " pdb=" N LEU C 529 " pdb=" C LEU C 529 " pdb=" CB LEU C 529 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.03e-01 ... (remaining 1540 not shown) Planarity restraints: 2940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV D 712 " -0.264 2.00e-02 2.50e+03 2.49e-01 6.20e+02 pdb=" C29 POV D 712 " 0.317 2.00e-02 2.50e+03 pdb="C210 POV D 712 " 0.169 2.00e-02 2.50e+03 pdb="C211 POV D 712 " -0.222 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 710 " -0.182 2.00e-02 2.50e+03 2.02e-01 4.07e+02 pdb=" C29 POV D 710 " 0.139 2.00e-02 2.50e+03 pdb="C210 POV D 710 " 0.255 2.00e-02 2.50e+03 pdb="C211 POV D 710 " -0.213 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C 605 " 0.089 2.00e-02 2.50e+03 1.99e-01 3.95e+02 pdb=" C29 POV C 605 " -0.262 2.00e-02 2.50e+03 pdb="C210 POV C 605 " 0.269 2.00e-02 2.50e+03 pdb="C211 POV C 605 " -0.095 2.00e-02 2.50e+03 ... (remaining 2937 not shown) Histogram of nonbonded interaction distances: 1.32 - 1.97: 298 1.97 - 2.63: 24285 2.63 - 3.29: 59395 3.29 - 3.94: 76095 3.94 - 4.60: 116726 Nonbonded interactions: 276799 Sorted by model distance: nonbonded pdb=" H ALA D 482 " pdb=" HH TYR D 495 " model vdw 1.317 2.100 nonbonded pdb="HD13 ILE D 302 " pdb=" HH TYR C 434 " model vdw 1.400 2.270 nonbonded pdb=" HG2 GLU D 420 " pdb=" HG SER D 498 " model vdw 1.452 2.270 nonbonded pdb=" HZ3 LYS D 607 " pdb="HG21 VAL D 611 " model vdw 1.470 2.270 nonbonded pdb=" HB3 ALA D 58 " pdb=" HZ3 LYS D 62 " model vdw 1.487 2.270 ... (remaining 276794 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 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: 0.110 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.920 Find NCS groups from input model: 0.060 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 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 : 0.008 0.083 10790 Z= 0.428 Angle : 0.895 17.592 14403 Z= 0.551 Chirality : 0.044 0.184 1543 Planarity : 0.015 0.249 1752 Dihedral : 20.445 176.563 4375 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.24), residues: 1218 helix: 0.62 (0.19), residues: 735 sheet: -0.54 (0.73), residues: 63 loop : -2.16 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 645 TYR 0.022 0.002 TYR D 98 PHE 0.027 0.002 PHE D 577 TRP 0.013 0.001 TRP C 78 HIS 0.005 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00754 (10790) covalent geometry : angle 0.89488 (14403) hydrogen bonds : bond 0.14902 ( 596) hydrogen bonds : angle 6.78326 ( 1755) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 ASN cc_start: 0.6256 (t0) cc_final: 0.5770 (t0) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2740 time to fit residues: 41.8043 Evaluate side-chains 87 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 523 ASN C 452 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.104227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.078104 restraints weight = 69868.193| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.31 r_work: 0.3376 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10790 Z= 0.165 Angle : 0.573 8.210 14403 Z= 0.310 Chirality : 0.039 0.161 1543 Planarity : 0.005 0.046 1752 Dihedral : 22.031 178.756 2064 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.96 % Allowed : 5.11 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.24), residues: 1218 helix: 1.12 (0.19), residues: 746 sheet: -0.55 (0.74), residues: 63 loop : -2.10 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 311 TYR 0.014 0.001 TYR C 434 PHE 0.016 0.001 PHE D 323 TRP 0.014 0.001 TRP C 78 HIS 0.004 0.001 HIS C 556 Details of bonding type rmsd covalent geometry : bond 0.00363 (10790) covalent geometry : angle 0.57302 (14403) hydrogen bonds : bond 0.06183 ( 596) hydrogen bonds : angle 5.15824 ( 1755) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 ASN cc_start: 0.6452 (t0) cc_final: 0.5900 (t0) outliers start: 10 outliers final: 5 residues processed: 96 average time/residue: 0.2532 time to fit residues: 33.9952 Evaluate side-chains 94 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain C residue 341 HIS Chi-restraints excluded: chain C residue 448 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 0 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 114 optimal weight: 0.0980 chunk 118 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.104165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.078211 restraints weight = 70428.273| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.30 r_work: 0.3379 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10790 Z= 0.129 Angle : 0.501 6.417 14403 Z= 0.273 Chirality : 0.037 0.148 1543 Planarity : 0.004 0.040 1752 Dihedral : 20.030 179.555 2064 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.67 % Allowed : 6.65 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.25), residues: 1218 helix: 1.44 (0.19), residues: 751 sheet: -0.69 (0.72), residues: 63 loop : -2.03 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 282 TYR 0.013 0.001 TYR C 434 PHE 0.017 0.001 PHE D 242 TRP 0.013 0.001 TRP C 78 HIS 0.004 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00266 (10790) covalent geometry : angle 0.50121 (14403) hydrogen bonds : bond 0.05634 ( 596) hydrogen bonds : angle 4.82327 ( 1755) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 223 ARG cc_start: 0.7935 (mmm160) cc_final: 0.7730 (mtp180) outliers start: 7 outliers final: 4 residues processed: 92 average time/residue: 0.2710 time to fit residues: 34.1252 Evaluate side-chains 85 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 341 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 112 optimal weight: 0.0970 chunk 55 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 452 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.103059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.076829 restraints weight = 70423.844| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.31 r_work: 0.3348 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10790 Z= 0.178 Angle : 0.532 7.907 14403 Z= 0.290 Chirality : 0.038 0.145 1543 Planarity : 0.004 0.043 1752 Dihedral : 19.765 177.040 2064 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.87 % Allowed : 7.51 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.24), residues: 1218 helix: 1.34 (0.19), residues: 749 sheet: -0.69 (0.72), residues: 63 loop : -2.11 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 282 TYR 0.014 0.001 TYR C 434 PHE 0.019 0.001 PHE D 323 TRP 0.012 0.001 TRP C 78 HIS 0.005 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00393 (10790) covalent geometry : angle 0.53226 (14403) hydrogen bonds : bond 0.05875 ( 596) hydrogen bonds : angle 4.83613 ( 1755) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 223 ARG cc_start: 0.7872 (mmm160) cc_final: 0.7614 (mtp180) REVERT: C 266 PHE cc_start: 0.7938 (t80) cc_final: 0.7497 (m-80) outliers start: 9 outliers final: 6 residues processed: 94 average time/residue: 0.2655 time to fit residues: 34.2842 Evaluate side-chains 92 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain C residue 341 HIS Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 112 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 GLN C 452 HIS C 516 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.101849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.075534 restraints weight = 70457.241| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.29 r_work: 0.3318 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10790 Z= 0.230 Angle : 0.573 7.572 14403 Z= 0.315 Chirality : 0.039 0.145 1543 Planarity : 0.004 0.047 1752 Dihedral : 19.828 179.857 2064 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.64 % Allowed : 8.86 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.24), residues: 1218 helix: 1.12 (0.18), residues: 748 sheet: -0.69 (0.71), residues: 63 loop : -2.19 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 282 TYR 0.016 0.002 TYR C 434 PHE 0.022 0.002 PHE D 323 TRP 0.011 0.002 TRP C 78 HIS 0.006 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00520 (10790) covalent geometry : angle 0.57310 (14403) hydrogen bonds : bond 0.06315 ( 596) hydrogen bonds : angle 4.93537 ( 1755) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 ASN cc_start: 0.6485 (t0) cc_final: 0.5966 (t0) REVERT: D 392 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.6946 (mp10) REVERT: C 223 ARG cc_start: 0.7929 (mmm160) cc_final: 0.7727 (mtp180) REVERT: C 266 PHE cc_start: 0.7975 (t80) cc_final: 0.7493 (m-80) outliers start: 17 outliers final: 11 residues processed: 100 average time/residue: 0.2615 time to fit residues: 36.2138 Evaluate side-chains 97 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 392 GLN Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 341 HIS Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 80 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 114 optimal weight: 0.0020 chunk 50 optimal weight: 3.9990 chunk 86 optimal weight: 0.0980 chunk 41 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN C 452 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.103334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.077109 restraints weight = 70228.285| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.32 r_work: 0.3353 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10790 Z= 0.126 Angle : 0.502 8.172 14403 Z= 0.276 Chirality : 0.037 0.178 1543 Planarity : 0.004 0.046 1752 Dihedral : 18.958 173.583 2064 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.16 % Allowed : 9.92 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.24), residues: 1218 helix: 1.50 (0.19), residues: 748 sheet: -0.72 (0.71), residues: 63 loop : -2.11 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 567 TYR 0.011 0.001 TYR C 434 PHE 0.014 0.001 PHE D 323 TRP 0.010 0.001 TRP C 78 HIS 0.003 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00258 (10790) covalent geometry : angle 0.50246 (14403) hydrogen bonds : bond 0.05696 ( 596) hydrogen bonds : angle 4.65357 ( 1755) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 ASN cc_start: 0.6486 (t0) cc_final: 0.5956 (t0) REVERT: D 392 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.6883 (mp10) REVERT: C 223 ARG cc_start: 0.7879 (mmm160) cc_final: 0.7609 (mtp180) REVERT: C 266 PHE cc_start: 0.7917 (t80) cc_final: 0.7464 (m-80) outliers start: 12 outliers final: 6 residues processed: 93 average time/residue: 0.2959 time to fit residues: 37.3396 Evaluate side-chains 94 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 392 GLN Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 341 HIS Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.102508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.076260 restraints weight = 70445.616| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.30 r_work: 0.3334 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10790 Z= 0.176 Angle : 0.527 8.167 14403 Z= 0.288 Chirality : 0.038 0.144 1543 Planarity : 0.004 0.044 1752 Dihedral : 18.914 171.939 2064 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.25 % Allowed : 9.83 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.24), residues: 1218 helix: 1.38 (0.19), residues: 751 sheet: -0.63 (0.73), residues: 61 loop : -2.17 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 503 TYR 0.013 0.001 TYR D 156 PHE 0.019 0.001 PHE D 323 TRP 0.012 0.001 TRP C 78 HIS 0.005 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00391 (10790) covalent geometry : angle 0.52675 (14403) hydrogen bonds : bond 0.05866 ( 596) hydrogen bonds : angle 4.69739 ( 1755) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 ASN cc_start: 0.6482 (t0) cc_final: 0.5963 (t0) REVERT: D 392 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.6984 (mp10) REVERT: C 223 ARG cc_start: 0.7912 (mmm160) cc_final: 0.7683 (mtp180) REVERT: C 266 PHE cc_start: 0.7951 (t80) cc_final: 0.7492 (m-80) REVERT: C 443 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8368 (mp0) outliers start: 13 outliers final: 8 residues processed: 96 average time/residue: 0.2749 time to fit residues: 35.8904 Evaluate side-chains 99 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 392 GLN Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 341 HIS Chi-restraints excluded: chain C residue 443 GLU Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 120 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.103303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.077125 restraints weight = 70181.043| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.32 r_work: 0.3354 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10790 Z= 0.131 Angle : 0.499 8.670 14403 Z= 0.272 Chirality : 0.037 0.143 1543 Planarity : 0.004 0.080 1752 Dihedral : 18.389 174.541 2064 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.35 % Allowed : 10.31 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.25), residues: 1218 helix: 1.57 (0.19), residues: 751 sheet: -0.62 (0.74), residues: 61 loop : -2.11 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 541 TYR 0.011 0.001 TYR C 434 PHE 0.015 0.001 PHE D 323 TRP 0.011 0.001 TRP C 78 HIS 0.003 0.001 HIS C 452 Details of bonding type rmsd covalent geometry : bond 0.00276 (10790) covalent geometry : angle 0.49933 (14403) hydrogen bonds : bond 0.05557 ( 596) hydrogen bonds : angle 4.55868 ( 1755) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 ASN cc_start: 0.6493 (t0) cc_final: 0.5974 (t0) REVERT: D 392 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.6938 (mp10) REVERT: C 223 ARG cc_start: 0.7861 (mmm160) cc_final: 0.7626 (mtp180) REVERT: C 266 PHE cc_start: 0.7925 (t80) cc_final: 0.7480 (m-80) REVERT: C 443 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8324 (pm20) outliers start: 14 outliers final: 9 residues processed: 94 average time/residue: 0.3050 time to fit residues: 38.0439 Evaluate side-chains 96 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 392 GLN Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 341 HIS Chi-restraints excluded: chain C residue 443 GLU Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 17 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.102489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.076232 restraints weight = 70099.731| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.30 r_work: 0.3336 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10790 Z= 0.178 Angle : 0.536 8.591 14403 Z= 0.291 Chirality : 0.038 0.143 1543 Planarity : 0.004 0.051 1752 Dihedral : 18.454 172.434 2064 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.16 % Allowed : 10.50 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.24), residues: 1218 helix: 1.44 (0.19), residues: 751 sheet: -0.63 (0.73), residues: 61 loop : -2.15 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 541 TYR 0.014 0.001 TYR C 19 PHE 0.020 0.001 PHE D 323 TRP 0.012 0.001 TRP C 78 HIS 0.004 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00396 (10790) covalent geometry : angle 0.53557 (14403) hydrogen bonds : bond 0.05796 ( 596) hydrogen bonds : angle 4.63501 ( 1755) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 ASN cc_start: 0.6480 (t0) cc_final: 0.5956 (t0) REVERT: D 392 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.6980 (mp10) REVERT: C 223 ARG cc_start: 0.7886 (mmm160) cc_final: 0.7657 (mtp180) REVERT: C 266 PHE cc_start: 0.7976 (t80) cc_final: 0.7506 (m-80) REVERT: C 443 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8332 (mp0) outliers start: 12 outliers final: 8 residues processed: 91 average time/residue: 0.2665 time to fit residues: 33.0192 Evaluate side-chains 96 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 392 GLN Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 443 GLU Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 112 optimal weight: 7.9990 chunk 98 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 31 optimal weight: 0.0970 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.102475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.076194 restraints weight = 70390.957| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.30 r_work: 0.3341 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10790 Z= 0.170 Angle : 0.529 8.614 14403 Z= 0.288 Chirality : 0.038 0.142 1543 Planarity : 0.004 0.045 1752 Dihedral : 18.318 171.836 2064 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.16 % Allowed : 10.50 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.24), residues: 1218 helix: 1.46 (0.19), residues: 751 sheet: -0.64 (0.72), residues: 61 loop : -2.17 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 541 TYR 0.014 0.001 TYR C 19 PHE 0.019 0.001 PHE D 375 TRP 0.011 0.001 TRP C 78 HIS 0.004 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00377 (10790) covalent geometry : angle 0.52917 (14403) hydrogen bonds : bond 0.05805 ( 596) hydrogen bonds : angle 4.60954 ( 1755) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 ASN cc_start: 0.6514 (t0) cc_final: 0.5980 (t0) REVERT: D 392 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.6985 (mp10) REVERT: C 223 ARG cc_start: 0.7836 (mmm160) cc_final: 0.7628 (mtp180) REVERT: C 266 PHE cc_start: 0.7940 (t80) cc_final: 0.7491 (m-80) outliers start: 12 outliers final: 9 residues processed: 92 average time/residue: 0.2761 time to fit residues: 34.3664 Evaluate side-chains 96 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 392 GLN Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 83 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.101167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.074788 restraints weight = 70727.889| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.30 r_work: 0.3300 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 10790 Z= 0.251 Angle : 0.601 8.168 14403 Z= 0.326 Chirality : 0.040 0.142 1543 Planarity : 0.004 0.043 1752 Dihedral : 18.855 174.140 2064 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.06 % Favored : 92.86 % Rotamer: Outliers : 0.87 % Allowed : 10.98 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.24), residues: 1218 helix: 1.14 (0.19), residues: 751 sheet: -0.40 (0.73), residues: 59 loop : -2.30 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 503 TYR 0.021 0.002 TYR C 19 PHE 0.028 0.002 PHE D 375 TRP 0.012 0.002 TRP C 78 HIS 0.008 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00575 (10790) covalent geometry : angle 0.60056 (14403) hydrogen bonds : bond 0.06391 ( 596) hydrogen bonds : angle 4.83204 ( 1755) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5654.95 seconds wall clock time: 96 minutes 24.31 seconds (5784.31 seconds total)