Starting phenix.real_space_refine on Thu Jul 2 23:46:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q7y_72319/07_2026/9q7y_72319_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q7y_72319/07_2026/9q7y_72319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q7y_72319/07_2026/9q7y_72319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q7y_72319/07_2026/9q7y_72319.map" model { file = "/net/cci-nas-00/data/ceres_data/9q7y_72319/07_2026/9q7y_72319_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q7y_72319/07_2026/9q7y_72319_neut.cif" } resolution = 3.35 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= 0.011 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 Ca 1 9.91 5 Zn 1 6.06 5 S 80 5.16 5 C 6661 2.51 5 N 1794 2.21 5 O 1993 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10530 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3731 Classifications: {'peptide': 462} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 436} Chain: "C" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "D" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 902 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "B" Number of atoms: 4980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 4980 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 21, 'TRANS': 607} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 85 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.80, per 1000 atoms: 0.17 Number of scatterers: 10530 At special positions: 0 Unit cell: (95.109, 113.225, 169.514, 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) Zn 1 29.99 Ca 1 19.99 S 80 16.00 O 1993 8.00 N 1794 7.00 C 6661 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 639 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 548 " distance=2.03 Simple disulfide: pdb=" SG CYS A 502 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 510 " - pdb=" SG CYS A 592 " distance=2.03 Simple disulfide: pdb=" SG CYS A 555 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS A 615 " distance=2.03 Simple disulfide: pdb=" SG CYS A 600 " - pdb=" SG CYS A 634 " distance=2.03 Simple disulfide: pdb=" SG CYS A 607 " - pdb=" SG CYS A 629 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 225 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 469 " distance=2.02 Simple disulfide: pdb=" SG CYS B 423 " - pdb=" SG CYS B 453 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 506 " distance=2.03 Simple disulfide: pdb=" SG CYS B 489 " - pdb=" SG CYS B 502 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 514 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 521 " - pdb=" SG CYS B 548 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 555 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 573 " distance=2.03 Simple disulfide: pdb=" SG CYS B 582 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 591 " - pdb=" SG CYS B 611 " distance=2.03 Simple disulfide: pdb=" SG CYS B 593 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 641 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG B 703 " - " ASN B 498 " " NAG B 704 " - " ASN B 551 " " NAG B 705 " - " ASN B 157 " " NAG B 706 " - " ASN B 264 " " NAG B 707 " - " ASN B 452 " " NAG B 708 " - " ASN B 594 " " NAG E 1 " - " ASN B 539 " Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 250.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 702 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 409 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 405 " pdb="ZN ZN B 702 " - pdb=" ND1 HIS B 415 " 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2446 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 19 sheets defined 30.0% alpha, 15.9% 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 374 through 381 Processing helix chain 'A' and resid 391 through 398 Processing helix chain 'A' and resid 405 through 425 Processing helix chain 'A' and resid 464 through 472 Processing helix chain 'A' and resid 475 through 480 Processing helix chain 'A' and resid 482 through 498 Processing helix chain 'A' and resid 514 through 518 Processing helix chain 'A' and resid 569 through 573 Processing helix chain 'A' and resid 611 through 618 Processing helix chain 'A' and resid 633 through 639 removed outlier: 3.769A pdb=" N ASP A 637 " --> pdb=" O HIS A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 659 removed outlier: 3.610A pdb=" N LEU A 658 " --> pdb=" O TYR A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 679 Processing helix chain 'A' and resid 679 through 688 Processing helix chain 'A' and resid 689 through 711 Processing helix chain 'A' and resid 719 through 736 removed outlier: 3.835A pdb=" N LEU A 730 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE A 731 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 732 " --> pdb=" O ALA A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 761 Processing helix chain 'A' and resid 769 through 785 Processing helix chain 'A' and resid 793 through 823 removed outlier: 3.728A pdb=" N LEU A 797 " --> pdb=" O GLY A 793 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.749A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.769A pdb=" N LYS D 65 " --> pdb=" O THR D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.819A pdb=" N THR D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 112 No H-bonds generated for 'chain 'B' and resid 110 through 112' Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 243 through 265 removed outlier: 3.789A pdb=" N THR B 247 " --> pdb=" O GLU B 243 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 261 " --> pdb=" O ARG B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 325 Processing helix chain 'B' and resid 325 through 330 removed outlier: 3.619A pdb=" N SER B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 347 removed outlier: 3.716A pdb=" N GLY B 346 " --> pdb=" O PHE B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 412 Processing helix chain 'B' and resid 445 through 449 removed outlier: 3.633A pdb=" N LYS B 448 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 465 Processing helix chain 'B' and resid 581 through 585 Processing helix chain 'B' and resid 647 through 659 Processing helix chain 'B' and resid 660 through 671 removed outlier: 3.523A pdb=" N PHE B 664 " --> pdb=" O SER B 660 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY B 665 " --> pdb=" O ILE B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 697 removed outlier: 3.932A pdb=" N SER B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) Proline residue: B 686 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 434 through 442 removed outlier: 3.676A pdb=" N VAL A 441 " --> pdb=" O GLU A 449 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 510 through 513 removed outlier: 3.518A pdb=" N VAL A 511 " --> pdb=" O CYS A 502 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 536 through 537 Processing sheet with id=AA4, first strand: chain 'A' and resid 555 through 557 removed outlier: 7.081A pdb=" N LYS A 578 " --> pdb=" O ASP A 556 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 606 through 610 removed outlier: 3.703A pdb=" N ARG A 606 " --> pdb=" O ILE A 601 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.536A pdb=" N SER C 67 " --> pdb=" O ASP C 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12 removed outlier: 7.164A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 6 through 8 Processing sheet with id=AA9, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.917A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.708A pdb=" N ARG D 98 " --> pdb=" O ASP D 107 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 68 through 73 removed outlier: 3.519A pdb=" N SER D 71 " --> pdb=" O TYR D 80 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 43 through 45 Processing sheet with id=AB4, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AB5, first strand: chain 'B' and resid 105 through 107 removed outlier: 4.256A pdb=" N VAL B 96 " --> pdb=" O TYR B 107 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 284 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N CYS B 225 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU B 280 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU B 227 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE B 282 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B 229 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE B 284 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA B 231 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LEU B 334 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS B 226 " --> pdb=" O LEU B 334 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N HIS B 336 " --> pdb=" O LYS B 226 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU B 228 " --> pdb=" O HIS B 336 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N PHE B 338 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL B 230 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 368 through 369 Processing sheet with id=AB7, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AB8, first strand: chain 'B' and resid 522 through 523 Processing sheet with id=AB9, first strand: chain 'B' and resid 533 through 535 removed outlier: 7.016A pdb=" N SER B 546 " --> pdb=" O CYS B 534 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 628 through 629 removed outlier: 4.119A pdb=" N LYS B 628 " --> pdb=" O CYS B 635 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS B 635 " --> pdb=" O LYS B 628 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 377 hydrogen bonds defined for protein. 1020 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: 1.50 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 1459 1.25 - 1.39: 2956 1.39 - 1.53: 5757 1.53 - 1.67: 504 1.67 - 1.81: 102 Bond restraints: 10778 Sorted by residual: bond pdb=" CG PRO B 220 " pdb=" CD PRO B 220 " ideal model delta sigma weight residual 1.503 1.105 0.398 3.40e-02 8.65e+02 1.37e+02 bond pdb=" CB PRO B 220 " pdb=" CG PRO B 220 " ideal model delta sigma weight residual 1.492 1.135 0.357 5.00e-02 4.00e+02 5.09e+01 bond pdb=" C1 NAG B 708 " pdb=" O5 NAG B 708 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" CB ASN B 157 " pdb=" CG ASN B 157 " ideal model delta sigma weight residual 1.516 1.442 0.074 2.50e-02 1.60e+03 8.66e+00 bond pdb=" N PRO B 220 " pdb=" CA PRO B 220 " ideal model delta sigma weight residual 1.469 1.498 -0.030 1.28e-02 6.10e+03 5.32e+00 ... (remaining 10773 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.76: 14587 14.76 - 29.52: 3 29.52 - 44.28: 0 44.28 - 59.04: 0 59.04 - 73.80: 1 Bond angle restraints: 14591 Sorted by residual: angle pdb=" CB PRO B 220 " pdb=" CG PRO B 220 " pdb=" CD PRO B 220 " ideal model delta sigma weight residual 106.10 179.90 -73.80 3.20e+00 9.77e-02 5.32e+02 angle pdb=" N PRO B 220 " pdb=" CD PRO B 220 " pdb=" CG PRO B 220 " ideal model delta sigma weight residual 103.20 74.75 28.45 1.50e+00 4.44e-01 3.60e+02 angle pdb=" CA PRO B 220 " pdb=" CB PRO B 220 " pdb=" CG PRO B 220 " ideal model delta sigma weight residual 104.50 76.20 28.30 1.90e+00 2.77e-01 2.22e+02 angle pdb=" N ASN B 157 " pdb=" CA ASN B 157 " pdb=" CB ASN B 157 " ideal model delta sigma weight residual 110.40 123.76 -13.36 1.63e+00 3.76e-01 6.71e+01 angle pdb=" C ASN B 157 " pdb=" CA ASN B 157 " pdb=" CB ASN B 157 " ideal model delta sigma weight residual 109.99 94.29 15.70 2.09e+00 2.29e-01 5.64e+01 ... (remaining 14586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.94: 5875 24.94 - 49.88: 604 49.88 - 74.82: 75 74.82 - 99.76: 25 99.76 - 124.70: 15 Dihedral angle restraints: 6594 sinusoidal: 2786 harmonic: 3808 Sorted by residual: dihedral pdb=" CB CYS B 521 " pdb=" SG CYS B 521 " pdb=" SG CYS B 548 " pdb=" CB CYS B 548 " ideal model delta sinusoidal sigma weight residual -86.00 -166.75 80.75 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS B 423 " pdb=" SG CYS B 423 " pdb=" SG CYS B 453 " pdb=" CB CYS B 453 " ideal model delta sinusoidal sigma weight residual 93.00 27.66 65.34 1 1.00e+01 1.00e-02 5.59e+01 dihedral pdb=" CB CYS B 542 " pdb=" SG CYS B 542 " pdb=" SG CYS B 573 " pdb=" CB CYS B 573 " ideal model delta sinusoidal sigma weight residual 93.00 32.97 60.03 1 1.00e+01 1.00e-02 4.80e+01 ... (remaining 6591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1490 0.086 - 0.171: 102 0.171 - 0.257: 6 0.257 - 0.343: 1 0.343 - 0.429: 1 Chirality restraints: 1600 Sorted by residual: chirality pdb=" C1 NAG B 705 " pdb=" ND2 ASN B 157 " pdb=" C2 NAG B 705 " pdb=" O5 NAG B 705 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" C1 NAG B 703 " pdb=" ND2 ASN B 498 " pdb=" C2 NAG B 703 " pdb=" O5 NAG B 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CA VAL B 156 " pdb=" N VAL B 156 " pdb=" C VAL B 156 " pdb=" CB VAL B 156 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1597 not shown) Planarity restraints: 1884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 157 " -0.047 2.00e-02 2.50e+03 5.91e-02 4.37e+01 pdb=" CG ASN B 157 " 0.110 2.00e-02 2.50e+03 pdb=" OD1 ASN B 157 " -0.048 2.00e-02 2.50e+03 pdb=" ND2 ASN B 157 " 0.011 2.00e-02 2.50e+03 pdb=" C1 NAG B 705 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 157 " -0.030 2.00e-02 2.50e+03 6.05e-02 3.66e+01 pdb=" CG ASN B 157 " 0.105 2.00e-02 2.50e+03 pdb=" OD1 ASN B 157 " -0.042 2.00e-02 2.50e+03 pdb=" ND2 ASN B 157 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 157 " 0.023 2.00e-02 2.50e+03 4.63e-02 2.15e+01 pdb=" C ASN B 157 " -0.080 2.00e-02 2.50e+03 pdb=" O ASN B 157 " 0.030 2.00e-02 2.50e+03 pdb=" N ASP B 158 " 0.027 2.00e-02 2.50e+03 ... (remaining 1881 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 551 2.72 - 3.27: 10458 3.27 - 3.81: 17038 3.81 - 4.35: 19913 4.35 - 4.90: 35027 Nonbonded interactions: 82987 Sorted by model distance: nonbonded pdb=" N GLU D 89 " pdb=" OE1 GLU D 89 " model vdw 2.175 3.120 nonbonded pdb=" OG1 THR C 94 " pdb=" OD2 ASP D 59 " model vdw 2.176 3.040 nonbonded pdb=" O CYS A 674 " pdb=" OG1 THR A 678 " model vdw 2.214 3.040 nonbonded pdb=" O THR A 571 " pdb=" OG SER A 630 " model vdw 2.225 3.040 nonbonded pdb=" O SER A 737 " pdb=" OG SER A 737 " model vdw 2.236 3.040 ... (remaining 82982 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: 14.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.870 Find NCS groups from input model: 0.040 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:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 : 0.007 0.398 10814 Z= 0.226 Angle : 0.991 73.803 14665 Z= 0.451 Chirality : 0.046 0.429 1600 Planarity : 0.005 0.098 1877 Dihedral : 19.889 124.701 4073 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.43 % Allowed : 32.93 % Favored : 66.64 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 7.02 % 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: 1305 helix: 1.59 (0.29), residues: 340 sheet: -0.83 (0.35), residues: 233 loop : -0.82 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 53 TYR 0.017 0.001 TYR B 495 PHE 0.014 0.001 PHE A 795 TRP 0.011 0.001 TRP A 460 HIS 0.007 0.001 HIS B 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.23 (10778) covalent geometry : angle 0.94069 / 0.44 (14591) SS BOND : bond 0.00243 / 0.16 ( 25) SS BOND : angle 1.01153 / 0.77 ( 50) hydrogen bonds : bond 0.19278 / 12.33 ( 372) hydrogen bonds : angle 7.19313 / 5.02 ( 1020) metal coordination : bond 0.00347 / 0.18 ( 3) link_BETA1-4 : bond 0.00011 / 0.01 ( 1) link_BETA1-4 : angle 2.18861 / 1.13 ( 3) link_NAG-ASN : bond 0.00665 / 0.31 ( 7) link_NAG-ASN : angle 8.19795 / 4.23 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 142 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 399 MET cc_start: 0.6127 (mmm) cc_final: 0.5637 (mmp) REVERT: A 734 LEU cc_start: 0.8838 (tp) cc_final: 0.8605 (tt) REVERT: A 798 TYR cc_start: 0.7534 (m-10) cc_final: 0.7309 (m-10) REVERT: A 825 TYR cc_start: 0.7195 (t80) cc_final: 0.6794 (t80) REVERT: C 81 GLU cc_start: 0.7898 (pp20) cc_final: 0.7672 (pp20) REVERT: D 105 GLU cc_start: 0.8773 (pm20) cc_final: 0.8571 (pm20) REVERT: B 160 LYS cc_start: 0.8599 (tmtt) cc_final: 0.8119 (mptt) REVERT: B 232 ASP cc_start: 0.8823 (p0) cc_final: 0.8503 (p0) outliers start: 5 outliers final: 3 residues processed: 146 average time/residue: 0.0845 time to fit residues: 18.0790 Evaluate side-chains 135 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 348 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 0.9980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 481 GLN A 531 HIS A 550 GLN A 564 HIS A 663 HIS A 723 GLN A 772 HIS C 27 GLN C 79 GLN D 111 GLN B 141 ASN B 341 GLN B 560 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.146115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.111904 restraints weight = 15754.605| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.88 r_work: 0.3191 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10814 Z= 0.155 Angle : 0.625 11.669 14665 Z= 0.312 Chirality : 0.045 0.296 1600 Planarity : 0.004 0.069 1877 Dihedral : 12.281 113.180 1601 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 4.67 % Allowed : 29.39 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: -0.30 (0.24), residues: 1305 helix: 1.55 (0.28), residues: 342 sheet: -0.92 (0.34), residues: 246 loop : -0.78 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 53 TYR 0.018 0.001 TYR B 369 PHE 0.011 0.001 PHE B 235 TRP 0.012 0.001 TRP B 312 HIS 0.005 0.001 HIS B 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (10778) covalent geometry : angle 0.59864 / 0.31 (14591) SS BOND : bond 0.00283 / 0.20 ( 25) SS BOND : angle 0.95316 / 0.67 ( 50) hydrogen bonds : bond 0.04314 / 2.85 ( 372) hydrogen bonds : angle 5.55012 / 3.92 ( 1020) metal coordination : bond 0.00179 / 0.09 ( 3) link_BETA1-4 : bond 0.00265 / 0.14 ( 1) link_BETA1-4 : angle 2.40432 / 1.26 ( 3) link_NAG-ASN : bond 0.00442 / 0.20 ( 7) link_NAG-ASN : angle 4.53230 / 2.65 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 142 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.6124 (mmm) cc_final: 0.5647 (mmp) REVERT: A 674 CYS cc_start: 0.8521 (OUTLIER) cc_final: 0.7841 (p) REVERT: A 734 LEU cc_start: 0.8864 (tp) cc_final: 0.8661 (tt) REVERT: A 784 PHE cc_start: 0.7321 (t80) cc_final: 0.7094 (t80) REVERT: A 825 TYR cc_start: 0.7282 (t80) cc_final: 0.6917 (t80) REVERT: C 81 GLU cc_start: 0.8113 (pp20) cc_final: 0.7796 (pp20) REVERT: D 73 ASP cc_start: 0.7871 (t0) cc_final: 0.7481 (t0) REVERT: D 76 LYS cc_start: 0.8882 (mtmm) cc_final: 0.8639 (mtmm) REVERT: B 160 LYS cc_start: 0.8860 (tmtt) cc_final: 0.8500 (mptt) REVERT: B 375 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8539 (mtpt) outliers start: 54 outliers final: 33 residues processed: 186 average time/residue: 0.0702 time to fit residues: 19.5135 Evaluate side-chains 163 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 674 CYS Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 603 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 113 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 27 GLN C 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.145591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.111133 restraints weight = 15869.631| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.95 r_work: 0.3189 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10814 Z= 0.161 Angle : 0.609 7.774 14665 Z= 0.303 Chirality : 0.044 0.243 1600 Planarity : 0.004 0.057 1877 Dihedral : 11.756 112.700 1599 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 6.14 % Allowed : 27.40 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: -0.30 (0.24), residues: 1305 helix: 1.53 (0.29), residues: 344 sheet: -0.81 (0.35), residues: 243 loop : -0.82 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 53 TYR 0.016 0.001 TYR B 369 PHE 0.013 0.001 PHE B 235 TRP 0.012 0.001 TRP A 460 HIS 0.005 0.001 HIS B 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (10778) covalent geometry : angle 0.59156 / 0.30 (14591) SS BOND : bond 0.00289 / 0.20 ( 25) SS BOND : angle 1.16447 / 0.83 ( 50) hydrogen bonds : bond 0.04209 / 2.76 ( 372) hydrogen bonds : angle 5.25414 / 3.70 ( 1020) metal coordination : bond 0.00152 / 0.08 ( 3) link_BETA1-4 : bond 0.01172 / 0.62 ( 1) link_BETA1-4 : angle 2.32775 / 1.22 ( 3) link_NAG-ASN : bond 0.00479 / 0.22 ( 7) link_NAG-ASN : angle 3.43403 / 2.11 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 131 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.6149 (mmm) cc_final: 0.5699 (mmp) REVERT: A 674 CYS cc_start: 0.8534 (OUTLIER) cc_final: 0.7859 (p) REVERT: A 784 PHE cc_start: 0.7323 (t80) cc_final: 0.6946 (t80) REVERT: A 798 TYR cc_start: 0.7590 (m-10) cc_final: 0.7388 (m-10) REVERT: A 825 TYR cc_start: 0.7218 (t80) cc_final: 0.6902 (t80) REVERT: C 81 GLU cc_start: 0.8239 (pp20) cc_final: 0.7867 (pp20) REVERT: D 76 LYS cc_start: 0.8923 (mtmm) cc_final: 0.8696 (mtmm) REVERT: B 160 LYS cc_start: 0.8926 (tmtt) cc_final: 0.8537 (mptt) REVERT: B 375 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8520 (mtpt) REVERT: B 484 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.7043 (m-30) REVERT: B 585 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6429 (pm20) outliers start: 71 outliers final: 54 residues processed: 191 average time/residue: 0.0646 time to fit residues: 18.8398 Evaluate side-chains 183 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 125 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 629 CYS Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 674 CYS Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 585 GLU Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 687 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 71 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 27 GLN C 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.144094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.109635 restraints weight = 15926.933| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.92 r_work: 0.3165 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10814 Z= 0.201 Angle : 0.616 7.420 14665 Z= 0.307 Chirality : 0.045 0.288 1600 Planarity : 0.004 0.052 1877 Dihedral : 10.519 109.608 1599 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 7.43 % Allowed : 26.53 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: -0.44 (0.24), residues: 1305 helix: 1.43 (0.28), residues: 344 sheet: -0.86 (0.35), residues: 238 loop : -0.93 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 53 TYR 0.018 0.001 TYR B 369 PHE 0.017 0.001 PHE B 235 TRP 0.013 0.002 TRP A 460 HIS 0.006 0.001 HIS B 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (10778) covalent geometry : angle 0.60029 / 0.30 (14591) SS BOND : bond 0.00329 / 0.22 ( 25) SS BOND : angle 1.11604 / 0.79 ( 50) hydrogen bonds : bond 0.04188 / 2.78 ( 372) hydrogen bonds : angle 5.12867 / 3.61 ( 1020) metal coordination : bond 0.00126 / 0.07 ( 3) link_BETA1-4 : bond 0.00594 / 0.31 ( 1) link_BETA1-4 : angle 2.15245 / 1.13 ( 3) link_NAG-ASN : bond 0.00499 / 0.22 ( 7) link_NAG-ASN : angle 3.26621 / 1.96 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 129 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.6163 (mmm) cc_final: 0.5748 (mmp) REVERT: A 674 CYS cc_start: 0.8496 (OUTLIER) cc_final: 0.7827 (p) REVERT: A 798 TYR cc_start: 0.7550 (m-10) cc_final: 0.6733 (t80) REVERT: A 825 TYR cc_start: 0.7188 (t80) cc_final: 0.6884 (t80) REVERT: C 81 GLU cc_start: 0.8307 (pp20) cc_final: 0.7891 (pp20) REVERT: D 38 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7523 (ptp-170) REVERT: D 76 LYS cc_start: 0.8951 (mtmm) cc_final: 0.8686 (mtmm) REVERT: B 160 LYS cc_start: 0.8916 (tmtt) cc_final: 0.8496 (mptt) REVERT: B 375 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8541 (mtpt) REVERT: B 585 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6368 (pm20) outliers start: 86 outliers final: 61 residues processed: 199 average time/residue: 0.0736 time to fit residues: 22.2180 Evaluate side-chains 185 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 120 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 629 CYS Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 674 CYS Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 585 GLU Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 680 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.144492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.103676 restraints weight = 15996.679| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.06 r_work: 0.3179 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10814 Z= 0.157 Angle : 0.604 8.716 14665 Z= 0.299 Chirality : 0.044 0.267 1600 Planarity : 0.004 0.048 1877 Dihedral : 10.408 121.675 1599 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 6.48 % Allowed : 27.31 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: -0.37 (0.24), residues: 1305 helix: 1.48 (0.28), residues: 344 sheet: -0.84 (0.35), residues: 238 loop : -0.88 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 53 TYR 0.015 0.001 TYR B 369 PHE 0.012 0.001 PHE B 235 TRP 0.012 0.001 TRP A 460 HIS 0.005 0.001 HIS B 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (10778) covalent geometry : angle 0.58607 / 0.30 (14591) SS BOND : bond 0.00257 / 0.17 ( 25) SS BOND : angle 1.00800 / 0.71 ( 50) hydrogen bonds : bond 0.03946 / 2.59 ( 372) hydrogen bonds : angle 5.00021 / 3.52 ( 1020) metal coordination : bond 0.00015 / 0.01 ( 3) link_BETA1-4 : bond 0.00653 / 0.34 ( 1) link_BETA1-4 : angle 2.07548 / 1.09 ( 3) link_NAG-ASN : bond 0.00557 / 0.26 ( 7) link_NAG-ASN : angle 3.56303 / 2.22 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 130 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.5996 (mmm) cc_final: 0.5621 (mmp) REVERT: A 408 TYR cc_start: 0.7237 (m-80) cc_final: 0.7008 (m-10) REVERT: A 674 CYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7700 (p) REVERT: A 749 PHE cc_start: 0.6285 (m-10) cc_final: 0.6070 (t80) REVERT: A 798 TYR cc_start: 0.7504 (m-10) cc_final: 0.6673 (t80) REVERT: A 825 TYR cc_start: 0.6991 (t80) cc_final: 0.6725 (t80) REVERT: C 81 GLU cc_start: 0.8336 (pp20) cc_final: 0.7914 (pp20) REVERT: D 38 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7263 (ptp-170) REVERT: B 160 LYS cc_start: 0.8826 (tmtt) cc_final: 0.8365 (mptt) REVERT: B 375 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8460 (mtpt) REVERT: B 585 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6273 (pm20) outliers start: 75 outliers final: 62 residues processed: 192 average time/residue: 0.0696 time to fit residues: 20.3471 Evaluate side-chains 189 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 123 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 629 CYS Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 674 CYS Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 582 CYS Chi-restraints excluded: chain B residue 585 GLU Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 680 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 68 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 128 optimal weight: 0.2980 chunk 81 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.145730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.105199 restraints weight = 15981.133| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.03 r_work: 0.3193 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10814 Z= 0.124 Angle : 0.571 7.622 14665 Z= 0.284 Chirality : 0.042 0.240 1600 Planarity : 0.004 0.045 1877 Dihedral : 10.039 121.130 1599 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 6.14 % Allowed : 27.74 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: -0.23 (0.24), residues: 1305 helix: 1.60 (0.28), residues: 344 sheet: -0.74 (0.35), residues: 238 loop : -0.79 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 53 TYR 0.013 0.001 TYR B 369 PHE 0.010 0.001 PHE B 581 TRP 0.011 0.001 TRP A 460 HIS 0.005 0.001 HIS B 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (10778) covalent geometry : angle 0.55514 / 0.28 (14591) SS BOND : bond 0.00283 / 0.22 ( 25) SS BOND : angle 0.87937 / 0.63 ( 50) hydrogen bonds : bond 0.03712 / 2.42 ( 372) hydrogen bonds : angle 4.84744 / 3.42 ( 1020) metal coordination : bond 0.00023 / 0.01 ( 3) link_BETA1-4 : bond 0.00890 / 0.47 ( 1) link_BETA1-4 : angle 1.97687 / 1.04 ( 3) link_NAG-ASN : bond 0.00538 / 0.25 ( 7) link_NAG-ASN : angle 3.31628 / 1.99 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 128 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.6131 (mmm) cc_final: 0.5558 (mmp) REVERT: A 408 TYR cc_start: 0.7259 (m-80) cc_final: 0.7027 (m-10) REVERT: A 674 CYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7709 (p) REVERT: A 798 TYR cc_start: 0.7425 (m-10) cc_final: 0.6663 (t80) REVERT: A 825 TYR cc_start: 0.7021 (t80) cc_final: 0.6772 (t80) REVERT: C 53 ARG cc_start: 0.7272 (ttm110) cc_final: 0.6532 (mtp180) REVERT: C 81 GLU cc_start: 0.8372 (pp20) cc_final: 0.7948 (pp20) REVERT: B 160 LYS cc_start: 0.8786 (tmtt) cc_final: 0.8368 (mptt) REVERT: B 585 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.6257 (pm20) outliers start: 71 outliers final: 57 residues processed: 184 average time/residue: 0.0644 time to fit residues: 17.9981 Evaluate side-chains 184 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 125 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 629 CYS Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 674 CYS Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 582 CYS Chi-restraints excluded: chain B residue 585 GLU Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 672 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 52 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 111 optimal weight: 0.4980 chunk 123 optimal weight: 8.9990 chunk 128 optimal weight: 0.7980 chunk 47 optimal weight: 0.2980 chunk 22 optimal weight: 0.8980 chunk 127 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 110 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.146854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.106224 restraints weight = 15961.499| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.10 r_work: 0.3213 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10814 Z= 0.110 Angle : 0.564 7.919 14665 Z= 0.280 Chirality : 0.042 0.211 1600 Planarity : 0.004 0.045 1877 Dihedral : 9.588 120.073 1599 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 5.27 % Allowed : 28.09 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: -0.12 (0.24), residues: 1305 helix: 1.69 (0.28), residues: 344 sheet: -0.65 (0.35), residues: 240 loop : -0.74 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 53 TYR 0.016 0.001 TYR B 495 PHE 0.014 0.001 PHE A 795 TRP 0.010 0.001 TRP A 460 HIS 0.004 0.001 HIS B 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (10778) covalent geometry : angle 0.54795 / 0.28 (14591) SS BOND : bond 0.00270 / 0.18 ( 25) SS BOND : angle 0.82240 / 0.59 ( 50) hydrogen bonds : bond 0.03541 / 2.30 ( 372) hydrogen bonds : angle 4.73585 / 3.34 ( 1020) metal coordination : bond 0.00029 / 0.01 ( 3) link_BETA1-4 : bond 0.00910 / 0.48 ( 1) link_BETA1-4 : angle 1.94812 / 1.02 ( 3) link_NAG-ASN : bond 0.00562 / 0.26 ( 7) link_NAG-ASN : angle 3.33390 / 1.96 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 134 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.6263 (mmm) cc_final: 0.5680 (mmp) REVERT: A 408 TYR cc_start: 0.7265 (m-80) cc_final: 0.7064 (m-10) REVERT: A 651 ASP cc_start: 0.8064 (p0) cc_final: 0.7849 (p0) REVERT: A 674 CYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7661 (p) REVERT: A 798 TYR cc_start: 0.7410 (m-10) cc_final: 0.6663 (t80) REVERT: A 825 TYR cc_start: 0.7021 (t80) cc_final: 0.6820 (t80) REVERT: C 53 ARG cc_start: 0.7348 (ttm110) cc_final: 0.6589 (mtp180) REVERT: C 81 GLU cc_start: 0.8400 (pp20) cc_final: 0.7980 (pp20) REVERT: D 73 ASP cc_start: 0.7668 (t0) cc_final: 0.7364 (t0) REVERT: D 76 LYS cc_start: 0.8737 (mtmm) cc_final: 0.8218 (mtmm) REVERT: B 160 LYS cc_start: 0.8758 (tmtt) cc_final: 0.8363 (mptt) REVERT: B 585 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.6384 (pm20) outliers start: 61 outliers final: 54 residues processed: 184 average time/residue: 0.0675 time to fit residues: 18.9188 Evaluate side-chains 185 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 129 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 629 CYS Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 674 CYS Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 539 ASN Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 582 CYS Chi-restraints excluded: chain B residue 585 GLU Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 672 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 23 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 27 GLN D 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.145573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.105079 restraints weight = 15886.743| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.03 r_work: 0.3186 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 : 0.003 0.036 10814 Z= 0.141 Angle : 0.585 8.399 14665 Z= 0.290 Chirality : 0.043 0.205 1600 Planarity : 0.004 0.044 1877 Dihedral : 9.248 119.236 1599 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 6.48 % Allowed : 27.31 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: -0.16 (0.24), residues: 1305 helix: 1.70 (0.28), residues: 344 sheet: -0.68 (0.35), residues: 246 loop : -0.78 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 53 TYR 0.015 0.001 TYR B 369 PHE 0.013 0.001 PHE A 781 TRP 0.012 0.001 TRP A 460 HIS 0.005 0.001 HIS B 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (10778) covalent geometry : angle 0.56972 / 0.29 (14591) SS BOND : bond 0.00244 / 0.16 ( 25) SS BOND : angle 0.90446 / 0.65 ( 50) hydrogen bonds : bond 0.03653 / 2.40 ( 372) hydrogen bonds : angle 4.75766 / 3.36 ( 1020) metal coordination : bond 0.00047 / 0.02 ( 3) link_BETA1-4 : bond 0.00830 / 0.44 ( 1) link_BETA1-4 : angle 1.85714 / 0.98 ( 3) link_NAG-ASN : bond 0.00529 / 0.25 ( 7) link_NAG-ASN : angle 3.36474 / 1.95 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 131 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.6256 (mmm) cc_final: 0.5694 (mmp) REVERT: A 674 CYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7669 (p) REVERT: A 798 TYR cc_start: 0.7345 (m-10) cc_final: 0.6655 (t80) REVERT: A 825 TYR cc_start: 0.6967 (t80) cc_final: 0.6751 (t80) REVERT: C 53 ARG cc_start: 0.7297 (ttm110) cc_final: 0.6537 (mtp180) REVERT: C 81 GLU cc_start: 0.8409 (pp20) cc_final: 0.7966 (pp20) REVERT: B 160 LYS cc_start: 0.8763 (tmtt) cc_final: 0.8370 (mptt) REVERT: B 494 MET cc_start: 0.8832 (ptp) cc_final: 0.8582 (ptp) REVERT: B 532 LYS cc_start: 0.7462 (ttmt) cc_final: 0.7169 (ttmt) REVERT: B 585 GLU cc_start: 0.6663 (OUTLIER) cc_final: 0.6316 (pm20) outliers start: 75 outliers final: 67 residues processed: 194 average time/residue: 0.0732 time to fit residues: 21.4392 Evaluate side-chains 198 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 129 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 629 CYS Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 674 CYS Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 539 ASN Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 582 CYS Chi-restraints excluded: chain B residue 585 GLU Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 672 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 40 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 23 optimal weight: 0.0670 chunk 62 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 77 optimal weight: 0.0270 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 27 GLN D 74 ASN D 111 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.147791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.107264 restraints weight = 15954.874| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.04 r_work: 0.3229 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10814 Z= 0.105 Angle : 0.566 8.524 14665 Z= 0.279 Chirality : 0.042 0.201 1600 Planarity : 0.003 0.044 1877 Dihedral : 8.846 118.033 1599 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 5.53 % Allowed : 27.74 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: 1305 helix: 1.83 (0.29), residues: 344 sheet: -0.56 (0.36), residues: 233 loop : -0.72 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 53 TYR 0.011 0.001 TYR A 789 PHE 0.011 0.001 PHE A 795 TRP 0.011 0.001 TRP D 47 HIS 0.004 0.001 HIS B 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (10778) covalent geometry : angle 0.54858 / 0.27 (14591) SS BOND : bond 0.00210 / 0.16 ( 25) SS BOND : angle 0.78813 / 0.57 ( 50) hydrogen bonds : bond 0.03403 / 2.21 ( 372) hydrogen bonds : angle 4.65162 / 3.27 ( 1020) metal coordination : bond 0.00065 / 0.03 ( 3) link_BETA1-4 : bond 0.00961 / 0.51 ( 1) link_BETA1-4 : angle 1.98656 / 1.05 ( 3) link_NAG-ASN : bond 0.00590 / 0.28 ( 7) link_NAG-ASN : angle 3.50218 / 1.98 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 130 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.6334 (mmm) cc_final: 0.5800 (mmp) REVERT: A 507 ARG cc_start: 0.6293 (ptp-170) cc_final: 0.6062 (ptt-90) REVERT: A 674 CYS cc_start: 0.8306 (t) cc_final: 0.7644 (p) REVERT: A 798 TYR cc_start: 0.7320 (m-10) cc_final: 0.6646 (t80) REVERT: C 81 GLU cc_start: 0.8426 (pp20) cc_final: 0.8021 (pp20) REVERT: D 46 GLU cc_start: 0.8423 (pt0) cc_final: 0.8100 (pm20) REVERT: D 73 ASP cc_start: 0.7619 (t0) cc_final: 0.7367 (t0) REVERT: D 76 LYS cc_start: 0.8730 (mtmm) cc_final: 0.7959 (mtmm) REVERT: B 494 MET cc_start: 0.8784 (ptp) cc_final: 0.8443 (ptp) REVERT: B 495 TYR cc_start: 0.7944 (m-10) cc_final: 0.7484 (m-10) REVERT: B 532 LYS cc_start: 0.7476 (ttmt) cc_final: 0.7198 (ttmt) REVERT: B 585 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6382 (pm20) outliers start: 64 outliers final: 57 residues processed: 185 average time/residue: 0.0731 time to fit residues: 20.4250 Evaluate side-chains 189 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 131 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 629 CYS Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 539 ASN Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 582 CYS Chi-restraints excluded: chain B residue 585 GLU Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 672 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 46 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 111 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 94 optimal weight: 0.4980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.146361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.105907 restraints weight = 15792.483| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.02 r_work: 0.3199 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10814 Z= 0.139 Angle : 0.583 8.567 14665 Z= 0.288 Chirality : 0.043 0.199 1600 Planarity : 0.004 0.044 1877 Dihedral : 8.694 117.747 1599 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 5.45 % Allowed : 27.74 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: -0.08 (0.24), residues: 1305 helix: 1.73 (0.29), residues: 345 sheet: -0.57 (0.36), residues: 233 loop : -0.74 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 53 TYR 0.015 0.001 TYR B 369 PHE 0.015 0.001 PHE A 795 TRP 0.011 0.001 TRP A 460 HIS 0.005 0.001 HIS B 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (10778) covalent geometry : angle 0.56552 / 0.28 (14591) SS BOND : bond 0.00220 / 0.14 ( 25) SS BOND : angle 0.86469 / 0.62 ( 50) hydrogen bonds : bond 0.03561 / 2.33 ( 372) hydrogen bonds : angle 4.68449 / 3.30 ( 1020) metal coordination : bond 0.00042 / 0.02 ( 3) link_BETA1-4 : bond 0.01023 / 0.54 ( 1) link_BETA1-4 : angle 1.90717 / 1.00 ( 3) link_NAG-ASN : bond 0.00540 / 0.25 ( 7) link_NAG-ASN : angle 3.55524 / 1.98 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 130 time to evaluate : 0.337 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: A 399 MET cc_start: 0.6341 (mmm) cc_final: 0.5804 (mmp) REVERT: A 674 CYS cc_start: 0.8340 (t) cc_final: 0.7677 (p) REVERT: A 798 TYR cc_start: 0.7302 (m-10) cc_final: 0.6649 (t80) REVERT: C 53 ARG cc_start: 0.7390 (ttm-80) cc_final: 0.7159 (ttm110) REVERT: C 81 GLU cc_start: 0.8431 (pp20) cc_final: 0.8019 (pp20) REVERT: D 73 ASP cc_start: 0.7693 (t0) cc_final: 0.7475 (t0) REVERT: B 494 MET cc_start: 0.8785 (ptp) cc_final: 0.8465 (ptp) REVERT: B 495 TYR cc_start: 0.7971 (m-10) cc_final: 0.7584 (m-10) REVERT: B 585 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6326 (pm20) outliers start: 63 outliers final: 59 residues processed: 183 average time/residue: 0.0683 time to fit residues: 18.9166 Evaluate side-chains 188 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 128 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 629 CYS Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 539 ASN Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 582 CYS Chi-restraints excluded: chain B residue 585 GLU Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 672 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 110 optimal weight: 1.9990 chunk 1 optimal weight: 0.0470 chunk 32 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 76 optimal weight: 0.0770 chunk 42 optimal weight: 2.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.148044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.107417 restraints weight = 15894.532| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.11 r_work: 0.3229 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10814 Z= 0.106 Angle : 0.576 8.825 14665 Z= 0.282 Chirality : 0.042 0.195 1600 Planarity : 0.003 0.044 1877 Dihedral : 8.427 116.895 1599 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 5.36 % Allowed : 28.18 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: 0.00 (0.24), residues: 1305 helix: 1.84 (0.29), residues: 344 sheet: -0.51 (0.36), residues: 232 loop : -0.71 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 53 TYR 0.012 0.001 TYR A 789 PHE 0.016 0.001 PHE A 795 TRP 0.011 0.001 TRP D 36 HIS 0.004 0.001 HIS B 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (10778) covalent geometry : angle 0.55816 / 0.28 (14591) SS BOND : bond 0.00179 / 0.12 ( 25) SS BOND : angle 0.79633 / 0.57 ( 50) hydrogen bonds : bond 0.03389 / 2.20 ( 372) hydrogen bonds : angle 4.61484 / 3.25 ( 1020) metal coordination : bond 0.00033 / 0.02 ( 3) link_BETA1-4 : bond 0.01085 / 0.57 ( 1) link_BETA1-4 : angle 1.92213 / 1.01 ( 3) link_NAG-ASN : bond 0.00594 / 0.28 ( 7) link_NAG-ASN : angle 3.66224 / 2.02 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2328.75 seconds wall clock time: 40 minutes 37.84 seconds (2437.84 seconds total)