Starting phenix.real_space_refine on Wed Feb 4 03:07:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o94_70241/02_2026/9o94_70241.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o94_70241/02_2026/9o94_70241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o94_70241/02_2026/9o94_70241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o94_70241/02_2026/9o94_70241.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o94_70241/02_2026/9o94_70241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o94_70241/02_2026/9o94_70241.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.031 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 6 5.49 5 Mg 2 5.21 5 S 36 5.16 5 C 5309 2.51 5 N 1442 2.21 5 O 1570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8365 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4194 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 21, 'TRANS': 530} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 4032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4032 Classifications: {'peptide': 538} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 20, 'TRANS': 517} Chain breaks: 1 Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 3, 'ASP:plan': 7, 'PHE:plan': 2, 'HIS:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 7} Unresolved non-hydrogen planarities: 121 Chain: "F" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 75 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.01, per 1000 atoms: 0.24 Number of scatterers: 8365 At special positions: 0 Unit cell: (74.3, 87.1787, 137.703, 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 36 16.00 P 6 15.00 Mg 2 11.99 O 1570 8.00 N 1442 7.00 C 5309 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: 0.53 Conformation dependent library (CDL) restraints added in 204.5 milliseconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 6 sheets defined 72.0% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 173 through 179 removed outlier: 4.126A pdb=" N CYS A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 183 through 203 removed outlier: 4.128A pdb=" N LEU A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 270 removed outlier: 3.770A pdb=" N LEU A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.523A pdb=" N GLN A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 290 Processing helix chain 'A' and resid 290 through 324 removed outlier: 4.438A pdb=" N SER A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 335 Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 339 through 346 Processing helix chain 'A' and resid 346 through 372 removed outlier: 3.648A pdb=" N GLN A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 380 removed outlier: 3.509A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 434 removed outlier: 4.014A pdb=" N GLU A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 403 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 475 removed outlier: 3.986A pdb=" N GLN A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Proline residue: A 466 - end of helix Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 573 through 580 Processing helix chain 'A' and resid 594 through 600 Processing helix chain 'A' and resid 608 through 619 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 644 through 658 Processing helix chain 'A' and resid 674 through 687 removed outlier: 4.009A pdb=" N LEU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLN A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 681 " --> pdb=" O SER A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 694 removed outlier: 3.787A pdb=" N ARG A 694 " --> pdb=" O ARG A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 707 removed outlier: 3.693A pdb=" N GLU A 707 " --> pdb=" O SER A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 733 removed outlier: 3.600A pdb=" N LYS A 733 " --> pdb=" O LEU A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 741 Processing helix chain 'B' and resid 139 through 146 Processing helix chain 'B' and resid 148 through 167 Processing helix chain 'B' and resid 168 through 181 removed outlier: 3.624A pdb=" N TYR B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 235 removed outlier: 3.652A pdb=" N SER B 191 " --> pdb=" O HIS B 187 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 244 Processing helix chain 'B' and resid 245 through 262 removed outlier: 4.462A pdb=" N THR B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU B 259 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 274 Processing helix chain 'B' and resid 274 through 289 Processing helix chain 'B' and resid 289 through 298 Processing helix chain 'B' and resid 302 through 338 removed outlier: 3.570A pdb=" N GLU B 316 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 347 through 398 removed outlier: 3.526A pdb=" N GLU B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 440 removed outlier: 4.432A pdb=" N ILE B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR B 415 " --> pdb=" O SER B 411 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 449 removed outlier: 3.615A pdb=" N PHE B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 517 Processing helix chain 'B' and resid 535 through 537 No H-bonds generated for 'chain 'B' and resid 535 through 537' Processing helix chain 'B' and resid 538 through 545 Processing helix chain 'B' and resid 560 through 564 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 592 removed outlier: 4.104A pdb=" N GLU B 591 " --> pdb=" O ASP B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 597 Processing helix chain 'B' and resid 601 through 605 Processing helix chain 'B' and resid 608 through 622 Processing helix chain 'B' and resid 638 through 645 Processing helix chain 'B' and resid 662 through 666 removed outlier: 3.625A pdb=" N THR B 665 " --> pdb=" O ARG B 662 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 7 Processing helix chain 'F' and resid 8 through 14 removed outlier: 4.221A pdb=" N UNK F 12 " --> pdb=" O UNK F 8 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 521 through 524 removed outlier: 5.973A pdb=" N GLN A 522 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N PHE A 510 " --> pdb=" O GLN A 522 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 521 through 524 removed outlier: 5.973A pdb=" N GLN A 522 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N PHE A 510 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL A 508 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLY A 559 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 581 through 583 removed outlier: 6.390A pdb=" N THR A 534 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL A 533 " --> pdb=" O HIS A 711 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N LEU A 713 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA A 535 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU A 715 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL A 537 " --> pdb=" O LEU A 715 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE A 712 " --> pdb=" O GLY A 723 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLY A 723 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE A 714 " --> pdb=" O ARG A 721 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 486 through 493 removed outlier: 6.746A pdb=" N LYS B 487 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SER B 474 " --> pdb=" O LYS B 487 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU B 489 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL B 473 " --> pdb=" O GLY B 524 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY B 524 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 546 through 549 removed outlier: 6.658A pdb=" N VAL B 498 " --> pdb=" O GLN B 671 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N LEU B 673 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA B 500 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU B 675 " --> pdb=" O ALA B 500 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL B 502 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 558 through 559 577 hydrogen bonds defined for protein. 1674 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.29 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1987 1.33 - 1.45: 1618 1.45 - 1.57: 4841 1.57 - 1.69: 10 1.69 - 1.81: 58 Bond restraints: 8514 Sorted by residual: bond pdb=" N PRO A 342 " pdb=" CD PRO A 342 " ideal model delta sigma weight residual 1.473 1.416 0.057 1.40e-02 5.10e+03 1.68e+01 bond pdb=" CA MET B 389 " pdb=" C MET B 389 " ideal model delta sigma weight residual 1.522 1.571 -0.049 1.39e-02 5.18e+03 1.24e+01 bond pdb=" N LEU B 459 " pdb=" CA LEU B 459 " ideal model delta sigma weight residual 1.456 1.496 -0.039 1.28e-02 6.10e+03 9.34e+00 bond pdb=" CZ ARG B 619 " pdb=" NH2 ARG B 619 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.32e+00 bond pdb=" CZ ARG B 561 " pdb=" NH2 ARG B 561 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 8.98e+00 ... (remaining 8509 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 11267 1.96 - 3.92: 250 3.92 - 5.88: 53 5.88 - 7.84: 10 7.84 - 9.81: 8 Bond angle restraints: 11588 Sorted by residual: angle pdb=" N GLN B 388 " pdb=" CA GLN B 388 " pdb=" C GLN B 388 " ideal model delta sigma weight residual 111.07 120.23 -9.16 1.07e+00 8.73e-01 7.33e+01 angle pdb=" N LEU B 392 " pdb=" CA LEU B 392 " pdb=" C LEU B 392 " ideal model delta sigma weight residual 111.36 102.84 8.52 1.09e+00 8.42e-01 6.11e+01 angle pdb=" PB ATP A1001 " pdb=" O3B ATP A1001 " pdb=" PG ATP A1001 " ideal model delta sigma weight residual 139.87 132.24 7.63 1.00e+00 1.00e+00 5.83e+01 angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 132.44 7.43 1.00e+00 1.00e+00 5.51e+01 angle pdb=" N LEU B 390 " pdb=" CA LEU B 390 " pdb=" CB LEU B 390 " ideal model delta sigma weight residual 110.01 119.82 -9.81 1.45e+00 4.76e-01 4.57e+01 ... (remaining 11583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4641 17.98 - 35.97: 317 35.97 - 53.95: 132 53.95 - 71.93: 17 71.93 - 89.92: 14 Dihedral angle restraints: 5121 sinusoidal: 1946 harmonic: 3175 Sorted by residual: dihedral pdb=" CA ASN B 563 " pdb=" C ASN B 563 " pdb=" N ILE B 564 " pdb=" CA ILE B 564 " ideal model delta harmonic sigma weight residual 180.00 151.34 28.66 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA HIS A 578 " pdb=" C HIS A 578 " pdb=" N ARG A 579 " pdb=" CA ARG A 579 " ideal model delta harmonic sigma weight residual 180.00 158.52 21.48 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" N LEU B 390 " pdb=" C LEU B 390 " pdb=" CA LEU B 390 " pdb=" CB LEU B 390 " ideal model delta harmonic sigma weight residual 122.80 132.84 -10.04 0 2.50e+00 1.60e-01 1.61e+01 ... (remaining 5118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1215 0.065 - 0.130: 131 0.130 - 0.195: 15 0.195 - 0.260: 2 0.260 - 0.325: 2 Chirality restraints: 1365 Sorted by residual: chirality pdb=" CA GLN B 388 " pdb=" N GLN B 388 " pdb=" C GLN B 388 " pdb=" CB GLN B 388 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA LEU B 390 " pdb=" N LEU B 390 " pdb=" C LEU B 390 " pdb=" CB LEU B 390 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA ILE B 564 " pdb=" N ILE B 564 " pdb=" C ILE B 564 " pdb=" CB ILE B 564 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1362 not shown) Planarity restraints: 1481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 428 " -0.045 2.00e-02 2.50e+03 8.49e-02 7.21e+01 pdb=" C TYR A 428 " 0.147 2.00e-02 2.50e+03 pdb=" O TYR A 428 " -0.054 2.00e-02 2.50e+03 pdb=" N ILE A 429 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 597 " 0.065 2.00e-02 2.50e+03 3.37e-02 2.27e+01 pdb=" CG TYR B 597 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B 597 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR B 597 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR B 597 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR B 597 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 597 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR B 597 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 566 " -0.039 2.00e-02 2.50e+03 2.89e-02 1.67e+01 pdb=" CG TYR B 566 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR B 566 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR B 566 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR B 566 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR B 566 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR B 566 " 0.020 2.00e-02 2.50e+03 pdb=" OH TYR B 566 " -0.056 2.00e-02 2.50e+03 ... (remaining 1478 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 16 2.56 - 3.14: 6623 3.14 - 3.73: 12623 3.73 - 4.31: 16740 4.31 - 4.90: 29194 Nonbonded interactions: 65196 Sorted by model distance: nonbonded pdb=" OG SER A 545 " pdb="MG MG A1002 " model vdw 1.975 2.170 nonbonded pdb=" OG SER B 510 " pdb="MG MG B 702 " model vdw 1.979 2.170 nonbonded pdb=" O3G ATP A1001 " pdb="MG MG A1002 " model vdw 1.999 2.170 nonbonded pdb=" OE1 GLN B 551 " pdb="MG MG B 702 " model vdw 2.029 2.170 nonbonded pdb=" OE1 GLN A 586 " pdb="MG MG A1002 " model vdw 2.037 2.170 ... (remaining 65191 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: 2.480 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: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.570 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 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 : 0.004 0.057 8514 Z= 0.236 Angle : 0.750 9.806 11588 Z= 0.468 Chirality : 0.044 0.325 1365 Planarity : 0.005 0.085 1481 Dihedral : 15.233 89.919 3081 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 0.47 % Allowed : 10.27 % Favored : 89.26 % Cbeta Deviations : 0.10 % 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: 2.60 (0.26), residues: 1082 helix: 2.15 (0.20), residues: 702 sheet: 2.41 (0.61), residues: 72 loop : 0.66 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 561 TYR 0.065 0.003 TYR B 597 PHE 0.028 0.002 PHE B 588 TRP 0.019 0.001 TRP A 413 HIS 0.004 0.001 HIS B 314 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 8514) covalent geometry : angle 0.75036 (11588) hydrogen bonds : bond 0.16346 ( 575) hydrogen bonds : angle 5.12032 ( 1674) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 0.303 Fit side-chains REVERT: A 301 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7932 (mm-30) REVERT: B 432 ASP cc_start: 0.8758 (t0) cc_final: 0.8541 (t0) outliers start: 4 outliers final: 3 residues processed: 100 average time/residue: 0.0745 time to fit residues: 10.7038 Evaluate side-chains 83 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 449 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 HIS B 518 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.113949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.093778 restraints weight = 11561.905| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.98 r_work: 0.2914 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8514 Z= 0.152 Angle : 0.517 7.009 11588 Z= 0.272 Chirality : 0.039 0.150 1365 Planarity : 0.004 0.035 1481 Dihedral : 8.224 83.145 1260 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.10 % Allowed : 9.80 % Favored : 88.10 % 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: 2.92 (0.26), residues: 1082 helix: 2.53 (0.19), residues: 717 sheet: 2.06 (0.60), residues: 74 loop : 0.41 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 483 TYR 0.015 0.001 TYR B 282 PHE 0.012 0.002 PHE A 275 TRP 0.011 0.001 TRP A 348 HIS 0.004 0.001 HIS B 314 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8514) covalent geometry : angle 0.51696 (11588) hydrogen bonds : bond 0.06639 ( 575) hydrogen bonds : angle 4.07420 ( 1674) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.324 Fit side-chains REVERT: A 565 ASP cc_start: 0.9027 (OUTLIER) cc_final: 0.8736 (m-30) REVERT: A 573 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.6834 (tm-30) REVERT: B 242 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7988 (mt0) REVERT: B 377 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8079 (mp) outliers start: 18 outliers final: 6 residues processed: 96 average time/residue: 0.0770 time to fit residues: 11.1048 Evaluate side-chains 90 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 387 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 98 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 82 optimal weight: 0.3980 chunk 106 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 58 optimal weight: 0.2980 chunk 67 optimal weight: 0.0870 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 GLN B 539 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.117601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.097417 restraints weight = 11468.387| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.97 r_work: 0.2967 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8514 Z= 0.113 Angle : 0.443 6.108 11588 Z= 0.234 Chirality : 0.036 0.140 1365 Planarity : 0.003 0.032 1481 Dihedral : 7.341 71.698 1254 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.75 % Allowed : 10.50 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.26 (0.26), residues: 1082 helix: 2.84 (0.19), residues: 717 sheet: 1.94 (0.61), residues: 74 loop : 0.46 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 483 TYR 0.012 0.001 TYR B 282 PHE 0.011 0.001 PHE B 588 TRP 0.010 0.001 TRP A 348 HIS 0.002 0.001 HIS B 314 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 8514) covalent geometry : angle 0.44298 (11588) hydrogen bonds : bond 0.05508 ( 575) hydrogen bonds : angle 3.73133 ( 1674) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.311 Fit side-chains REVERT: A 339 PHE cc_start: 0.8036 (m-80) cc_final: 0.7744 (m-80) REVERT: A 565 ASP cc_start: 0.9054 (OUTLIER) cc_final: 0.8776 (m-30) REVERT: B 242 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7912 (mt0) REVERT: B 377 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8034 (mp) REVERT: B 432 ASP cc_start: 0.8771 (t0) cc_final: 0.8551 (t0) outliers start: 15 outliers final: 5 residues processed: 97 average time/residue: 0.0666 time to fit residues: 9.9989 Evaluate side-chains 90 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 377 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 19 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 539 HIS B 643 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.116086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.095952 restraints weight = 11656.110| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.99 r_work: 0.2944 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8514 Z= 0.119 Angle : 0.443 5.590 11588 Z= 0.233 Chirality : 0.037 0.145 1365 Planarity : 0.003 0.035 1481 Dihedral : 7.259 76.400 1254 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.68 % Allowed : 9.68 % Favored : 87.63 % 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: 3.37 (0.26), residues: 1082 helix: 2.96 (0.19), residues: 717 sheet: 1.90 (0.61), residues: 74 loop : 0.43 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 483 TYR 0.009 0.001 TYR B 282 PHE 0.011 0.001 PHE A 275 TRP 0.008 0.001 TRP A 348 HIS 0.003 0.001 HIS B 539 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8514) covalent geometry : angle 0.44267 (11588) hydrogen bonds : bond 0.05555 ( 575) hydrogen bonds : angle 3.66982 ( 1674) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.215 Fit side-chains REVERT: A 339 PHE cc_start: 0.8075 (m-80) cc_final: 0.7853 (m-80) REVERT: A 565 ASP cc_start: 0.9152 (OUTLIER) cc_final: 0.8877 (m-30) REVERT: A 573 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.6715 (tm-30) REVERT: B 242 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7864 (mt0) REVERT: B 377 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8117 (mp) REVERT: B 380 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7618 (ttm170) REVERT: B 432 ASP cc_start: 0.8810 (t0) cc_final: 0.8537 (t0) outliers start: 23 outliers final: 9 residues processed: 99 average time/residue: 0.0634 time to fit residues: 9.6835 Evaluate side-chains 93 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 548 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 0 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 44 optimal weight: 0.2980 chunk 16 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 539 HIS B 643 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.115931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.095804 restraints weight = 11543.266| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.98 r_work: 0.2942 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8514 Z= 0.119 Angle : 0.435 5.608 11588 Z= 0.230 Chirality : 0.037 0.144 1365 Planarity : 0.003 0.033 1481 Dihedral : 7.230 79.243 1254 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.75 % Allowed : 11.55 % Favored : 86.70 % 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: 3.42 (0.26), residues: 1082 helix: 3.00 (0.19), residues: 717 sheet: 1.84 (0.61), residues: 74 loop : 0.46 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 483 TYR 0.009 0.001 TYR B 172 PHE 0.011 0.001 PHE A 275 TRP 0.008 0.001 TRP A 348 HIS 0.003 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 8514) covalent geometry : angle 0.43534 (11588) hydrogen bonds : bond 0.05507 ( 575) hydrogen bonds : angle 3.62948 ( 1674) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.223 Fit side-chains REVERT: A 339 PHE cc_start: 0.8002 (m-80) cc_final: 0.7786 (m-80) REVERT: A 565 ASP cc_start: 0.9205 (OUTLIER) cc_final: 0.8870 (m-30) REVERT: A 573 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.6741 (tm-30) REVERT: B 242 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7826 (mt0) REVERT: B 377 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8055 (mp) REVERT: B 422 TYR cc_start: 0.8140 (t80) cc_final: 0.7796 (t80) REVERT: B 432 ASP cc_start: 0.8825 (t0) cc_final: 0.8539 (t0) outliers start: 15 outliers final: 9 residues processed: 91 average time/residue: 0.0657 time to fit residues: 9.0027 Evaluate side-chains 91 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 548 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 84 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 539 HIS B 643 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.117151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.096909 restraints weight = 11393.797| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.99 r_work: 0.2960 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8514 Z= 0.110 Angle : 0.420 5.628 11588 Z= 0.224 Chirality : 0.036 0.161 1365 Planarity : 0.003 0.032 1481 Dihedral : 7.080 78.622 1254 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.22 % Allowed : 11.32 % Favored : 86.46 % 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: 3.53 (0.26), residues: 1082 helix: 3.08 (0.19), residues: 717 sheet: 1.77 (0.61), residues: 76 loop : 0.53 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 483 TYR 0.008 0.001 TYR B 172 PHE 0.010 0.001 PHE A 624 TRP 0.008 0.001 TRP A 348 HIS 0.003 0.001 HIS B 539 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 8514) covalent geometry : angle 0.42026 (11588) hydrogen bonds : bond 0.05191 ( 575) hydrogen bonds : angle 3.55410 ( 1674) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.226 Fit side-chains REVERT: A 565 ASP cc_start: 0.9251 (OUTLIER) cc_final: 0.8948 (m-30) REVERT: A 573 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.6729 (tm-30) REVERT: B 242 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7852 (mt0) REVERT: B 377 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8122 (mp) REVERT: B 380 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7846 (ttm170) REVERT: B 422 TYR cc_start: 0.8129 (t80) cc_final: 0.7814 (t80) REVERT: B 432 ASP cc_start: 0.8874 (t0) cc_final: 0.8592 (t0) outliers start: 19 outliers final: 10 residues processed: 93 average time/residue: 0.0593 time to fit residues: 8.5368 Evaluate side-chains 94 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 548 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 40 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 = 0.3363 r_free = 0.3363 target = 0.117349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.097143 restraints weight = 11525.302| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.99 r_work: 0.2965 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8514 Z= 0.110 Angle : 0.426 6.289 11588 Z= 0.226 Chirality : 0.036 0.141 1365 Planarity : 0.003 0.032 1481 Dihedral : 7.028 79.109 1254 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.87 % Allowed : 12.02 % Favored : 86.11 % 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: 3.58 (0.26), residues: 1082 helix: 3.12 (0.19), residues: 717 sheet: 1.79 (0.61), residues: 76 loop : 0.55 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 483 TYR 0.008 0.001 TYR B 172 PHE 0.010 0.001 PHE B 588 TRP 0.008 0.001 TRP A 348 HIS 0.003 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 8514) covalent geometry : angle 0.42617 (11588) hydrogen bonds : bond 0.05128 ( 575) hydrogen bonds : angle 3.52514 ( 1674) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.314 Fit side-chains REVERT: A 565 ASP cc_start: 0.9244 (OUTLIER) cc_final: 0.8933 (m-30) REVERT: A 573 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.6685 (tm-30) REVERT: B 242 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7756 (mt0) REVERT: B 377 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8067 (mp) REVERT: B 380 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7754 (ttm170) REVERT: B 422 TYR cc_start: 0.8088 (t80) cc_final: 0.7802 (t80) REVERT: B 432 ASP cc_start: 0.8840 (t0) cc_final: 0.8562 (t0) outliers start: 16 outliers final: 11 residues processed: 93 average time/residue: 0.0581 time to fit residues: 8.4212 Evaluate side-chains 100 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 548 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 91 optimal weight: 0.0970 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 539 HIS B 590 GLN B 643 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.117277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.096988 restraints weight = 11459.045| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.00 r_work: 0.2962 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8514 Z= 0.110 Angle : 0.418 5.649 11588 Z= 0.222 Chirality : 0.036 0.142 1365 Planarity : 0.003 0.032 1481 Dihedral : 7.010 79.735 1254 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.98 % Allowed : 12.49 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.61 (0.26), residues: 1082 helix: 3.17 (0.19), residues: 711 sheet: 1.80 (0.61), residues: 76 loop : 0.56 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 483 TYR 0.009 0.001 TYR B 172 PHE 0.010 0.001 PHE B 588 TRP 0.007 0.001 TRP A 348 HIS 0.003 0.001 HIS B 314 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 8514) covalent geometry : angle 0.41796 (11588) hydrogen bonds : bond 0.05101 ( 575) hydrogen bonds : angle 3.51945 ( 1674) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.202 Fit side-chains REVERT: A 565 ASP cc_start: 0.9231 (OUTLIER) cc_final: 0.8834 (m-30) REVERT: A 573 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.6743 (tm-30) REVERT: B 242 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7809 (mt0) REVERT: B 282 TYR cc_start: 0.7984 (t80) cc_final: 0.7681 (t80) REVERT: B 284 PHE cc_start: 0.6813 (m-10) cc_final: 0.6578 (m-10) REVERT: B 377 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8115 (mp) REVERT: B 380 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7793 (ttm170) REVERT: B 422 TYR cc_start: 0.8061 (t80) cc_final: 0.7787 (t80) REVERT: B 432 ASP cc_start: 0.8868 (t0) cc_final: 0.8610 (t0) outliers start: 17 outliers final: 11 residues processed: 93 average time/residue: 0.0635 time to fit residues: 8.9340 Evaluate side-chains 98 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 548 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 69 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 539 HIS B 643 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.115757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.095551 restraints weight = 11508.491| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.98 r_work: 0.2936 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8514 Z= 0.121 Angle : 0.433 5.660 11588 Z= 0.230 Chirality : 0.037 0.146 1365 Planarity : 0.003 0.032 1481 Dihedral : 7.139 82.706 1254 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.22 % Allowed : 12.25 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.56 (0.26), residues: 1082 helix: 3.12 (0.19), residues: 717 sheet: 1.78 (0.60), residues: 77 loop : 0.50 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 483 TYR 0.010 0.001 TYR B 172 PHE 0.011 0.001 PHE B 157 TRP 0.007 0.001 TRP A 348 HIS 0.003 0.001 HIS B 539 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8514) covalent geometry : angle 0.43348 (11588) hydrogen bonds : bond 0.05441 ( 575) hydrogen bonds : angle 3.57985 ( 1674) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.313 Fit side-chains REVERT: A 565 ASP cc_start: 0.9220 (OUTLIER) cc_final: 0.8757 (m-30) REVERT: A 573 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.6813 (tm-30) REVERT: B 242 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7827 (mt0) REVERT: B 284 PHE cc_start: 0.6785 (m-10) cc_final: 0.6502 (m-80) REVERT: B 377 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8129 (mp) REVERT: B 380 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7797 (ttm170) REVERT: B 422 TYR cc_start: 0.8070 (t80) cc_final: 0.7770 (t80) REVERT: B 432 ASP cc_start: 0.8853 (t0) cc_final: 0.8611 (t0) outliers start: 19 outliers final: 13 residues processed: 91 average time/residue: 0.0631 time to fit residues: 8.9118 Evaluate side-chains 96 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 548 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 18 optimal weight: 0.0670 chunk 54 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 539 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.117476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.097354 restraints weight = 11464.381| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.97 r_work: 0.2954 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8514 Z= 0.112 Angle : 0.431 6.910 11588 Z= 0.229 Chirality : 0.036 0.141 1365 Planarity : 0.003 0.032 1481 Dihedral : 7.051 81.377 1254 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.98 % Allowed : 12.60 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.59 (0.26), residues: 1082 helix: 3.17 (0.19), residues: 711 sheet: 1.78 (0.61), residues: 76 loop : 0.51 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 483 TYR 0.019 0.001 TYR B 282 PHE 0.010 0.001 PHE B 588 TRP 0.008 0.001 TRP A 348 HIS 0.003 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 8514) covalent geometry : angle 0.43067 (11588) hydrogen bonds : bond 0.05196 ( 575) hydrogen bonds : angle 3.53927 ( 1674) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.320 Fit side-chains REVERT: A 565 ASP cc_start: 0.9209 (OUTLIER) cc_final: 0.8831 (m-30) REVERT: A 573 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.6770 (tm-30) REVERT: B 242 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7858 (mt0) REVERT: B 284 PHE cc_start: 0.6762 (m-10) cc_final: 0.6485 (m-80) REVERT: B 377 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8105 (mp) REVERT: B 380 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7776 (ttm170) REVERT: B 422 TYR cc_start: 0.8046 (t80) cc_final: 0.7773 (t80) REVERT: B 432 ASP cc_start: 0.8842 (t0) cc_final: 0.8541 (t0) outliers start: 17 outliers final: 11 residues processed: 90 average time/residue: 0.0689 time to fit residues: 9.6086 Evaluate side-chains 96 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 548 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 539 HIS B 643 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.111552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.091514 restraints weight = 11605.199| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.97 r_work: 0.2875 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8514 Z= 0.187 Angle : 0.512 5.661 11588 Z= 0.273 Chirality : 0.040 0.296 1365 Planarity : 0.003 0.035 1481 Dihedral : 7.612 89.779 1254 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.22 % Allowed : 12.60 % Favored : 85.18 % Cbeta Deviations : 0.10 % 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: 3.20 (0.26), residues: 1082 helix: 2.86 (0.19), residues: 716 sheet: 1.66 (0.59), residues: 77 loop : 0.33 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 561 TYR 0.015 0.001 TYR B 282 PHE 0.014 0.002 PHE A 275 TRP 0.010 0.001 TRP B 263 HIS 0.005 0.001 HIS B 314 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 8514) covalent geometry : angle 0.51172 (11588) hydrogen bonds : bond 0.06635 ( 575) hydrogen bonds : angle 3.83343 ( 1674) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1825.68 seconds wall clock time: 31 minutes 53.21 seconds (1913.21 seconds total)