Starting phenix.real_space_refine on Sun May 3 05:10:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q7y_72319/05_2026/9q7y_72319_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q7y_72319/05_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_72319/05_2026/9q7y_72319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q7y_72319/05_2026/9q7y_72319.map" model { file = "/net/cci-nas-00/data/ceres_data/9q7y_72319/05_2026/9q7y_72319_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q7y_72319/05_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-2.1rc2-6044/lib/python3.9/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, 86 Unusual residues: {' CA': 1, ' ZN': 1, 'NAG': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 2.55, per 1000 atoms: 0.24 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: 0.84 Conformation dependent library (CDL) restraints added in 376.4 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: 0.39 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: 1.75 Time building geometry restraints manager: 1.12 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: 17.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.010 Process input model: 12.340 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 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 covalent geometry : bond 0.00655 (10778) covalent geometry : angle 0.94069 (14591) SS BOND : bond 0.00243 ( 25) SS BOND : angle 1.01153 ( 50) hydrogen bonds : bond 0.19278 ( 372) hydrogen bonds : angle 7.19313 ( 1020) metal coordination : bond 0.00347 ( 3) link_BETA1-4 : bond 0.00011 ( 1) link_BETA1-4 : angle 2.18861 ( 3) link_NAG-ASN : bond 0.00665 ( 7) link_NAG-ASN : angle 8.19795 ( 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 : 0.414 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: 0.0964 time to fit residues: 20.6545 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 : 0.403 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.146066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112022 restraints weight = 15726.975| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.04 r_work: 0.3200 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10814 Z= 0.156 Angle : 0.623 11.152 14665 Z= 0.311 Chirality : 0.045 0.272 1600 Planarity : 0.004 0.069 1877 Dihedral : 12.317 113.493 1601 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.58 % Allowed : 29.56 % Favored : 65.86 % 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: -0.31 (0.24), residues: 1305 helix: 1.54 (0.28), residues: 342 sheet: -0.93 (0.34), residues: 246 loop : -0.78 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 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 covalent geometry : bond 0.00363 (10778) covalent geometry : angle 0.59696 (14591) SS BOND : bond 0.00281 ( 25) SS BOND : angle 0.96039 ( 50) hydrogen bonds : bond 0.04385 ( 372) hydrogen bonds : angle 5.56563 ( 1020) metal coordination : bond 0.00148 ( 3) link_BETA1-4 : bond 0.00530 ( 1) link_BETA1-4 : angle 2.32809 ( 3) link_NAG-ASN : bond 0.00941 ( 7) link_NAG-ASN : angle 4.51000 ( 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 195 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 142 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.6115 (mmm) cc_final: 0.5639 (mmp) REVERT: A 674 CYS cc_start: 0.8532 (OUTLIER) cc_final: 0.7856 (p) REVERT: A 734 LEU cc_start: 0.8864 (tp) cc_final: 0.8660 (tt) REVERT: A 784 PHE cc_start: 0.7320 (t80) cc_final: 0.7098 (t80) REVERT: A 825 TYR cc_start: 0.7277 (t80) cc_final: 0.6915 (t80) REVERT: C 53 ARG cc_start: 0.6876 (mtm110) cc_final: 0.6668 (ttm-80) REVERT: C 81 GLU cc_start: 0.8109 (pp20) cc_final: 0.7792 (pp20) REVERT: D 73 ASP cc_start: 0.7884 (t0) cc_final: 0.7498 (t0) REVERT: D 76 LYS cc_start: 0.8886 (mtmm) cc_final: 0.8645 (mtmm) REVERT: B 160 LYS cc_start: 0.8850 (tmtt) cc_final: 0.8496 (mptt) REVERT: B 375 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8545 (mtpt) outliers start: 53 outliers final: 32 residues processed: 185 average time/residue: 0.0918 time to fit residues: 25.4607 Evaluate side-chains 161 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 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: 0.0570 chunk 122 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 63 optimal weight: 0.4980 chunk 78 optimal weight: 0.0570 chunk 64 optimal weight: 0.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3861 r_free = 0.3861 target = 0.147841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.113399 restraints weight = 15814.330| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.97 r_work: 0.3225 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10814 Z= 0.113 Angle : 0.583 7.709 14665 Z= 0.289 Chirality : 0.043 0.235 1600 Planarity : 0.004 0.056 1877 Dihedral : 11.788 119.919 1599 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.75 % Allowed : 28.35 % Favored : 66.90 % 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: -0.18 (0.24), residues: 1305 helix: 1.61 (0.29), residues: 344 sheet: -0.71 (0.35), residues: 243 loop : -0.74 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 382 TYR 0.012 0.001 TYR B 369 PHE 0.011 0.001 PHE B 581 TRP 0.011 0.001 TRP A 460 HIS 0.004 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00251 (10778) covalent geometry : angle 0.56555 (14591) SS BOND : bond 0.00228 ( 25) SS BOND : angle 1.16130 ( 50) hydrogen bonds : bond 0.03955 ( 372) hydrogen bonds : angle 5.18462 ( 1020) metal coordination : bond 0.00176 ( 3) link_BETA1-4 : bond 0.00789 ( 1) link_BETA1-4 : angle 2.59686 ( 3) link_NAG-ASN : bond 0.00501 ( 7) link_NAG-ASN : angle 3.28424 ( 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 190 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 135 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.6167 (mmm) cc_final: 0.5714 (mmp) REVERT: A 674 CYS cc_start: 0.8496 (OUTLIER) cc_final: 0.7812 (p) REVERT: A 677 MET cc_start: 0.8232 (mmt) cc_final: 0.8021 (mmp) REVERT: A 784 PHE cc_start: 0.7306 (t80) cc_final: 0.6930 (t80) REVERT: A 798 TYR cc_start: 0.7566 (m-10) cc_final: 0.7362 (m-10) REVERT: C 81 GLU cc_start: 0.8203 (pp20) cc_final: 0.7874 (pp20) REVERT: B 160 LYS cc_start: 0.8908 (tmtt) cc_final: 0.8535 (mptt) REVERT: B 487 GLU cc_start: 0.8587 (pm20) cc_final: 0.7983 (pm20) REVERT: B 585 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6449 (pm20) outliers start: 55 outliers final: 41 residues processed: 182 average time/residue: 0.0859 time to fit residues: 23.5878 Evaluate side-chains 173 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 629 CYS Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 674 CYS Chi-restraints excluded: chain A residue 683 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 51 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 84 THR 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 348 LEU 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 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 560 ASN 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: 0.0870 chunk 2 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN C 27 GLN C 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.145118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110623 restraints weight = 15895.160| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.91 r_work: 0.3181 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10814 Z= 0.182 Angle : 0.600 7.418 14665 Z= 0.299 Chirality : 0.045 0.289 1600 Planarity : 0.004 0.050 1877 Dihedral : 10.438 110.729 1599 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 6.83 % Allowed : 26.88 % Favored : 66.29 % 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: 1.52 (0.28), residues: 344 sheet: -0.72 (0.35), residues: 238 loop : -0.86 (0.23), residues: 723 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 0.016 0.001 PHE B 235 TRP 0.013 0.001 TRP A 460 HIS 0.006 0.001 HIS B 415 Details of bonding type rmsd covalent geometry : bond 0.00431 (10778) covalent geometry : angle 0.58396 (14591) SS BOND : bond 0.00297 ( 25) SS BOND : angle 1.09706 ( 50) hydrogen bonds : bond 0.04081 ( 372) hydrogen bonds : angle 5.07300 ( 1020) metal coordination : bond 0.00101 ( 3) link_BETA1-4 : bond 0.01029 ( 1) link_BETA1-4 : angle 2.13378 ( 3) link_NAG-ASN : bond 0.00513 ( 7) link_NAG-ASN : angle 3.24888 ( 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 217 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 138 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.6256 (mmm) cc_final: 0.5824 (mmp) REVERT: A 674 CYS cc_start: 0.8565 (OUTLIER) cc_final: 0.7878 (p) REVERT: A 798 TYR cc_start: 0.7471 (m-10) cc_final: 0.6698 (t80) REVERT: A 825 TYR cc_start: 0.7257 (t80) cc_final: 0.6950 (t80) REVERT: C 81 GLU cc_start: 0.8296 (pp20) cc_final: 0.7888 (pp20) REVERT: B 160 LYS cc_start: 0.8934 (tmtt) cc_final: 0.8594 (mptt) REVERT: B 375 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8535 (mtpt) REVERT: B 487 GLU cc_start: 0.8626 (pm20) cc_final: 0.7980 (pm20) REVERT: B 585 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6397 (pm20) outliers start: 79 outliers final: 61 residues processed: 202 average time/residue: 0.0864 time to fit residues: 26.3294 Evaluate side-chains 191 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 127 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 722 SER Chi-restraints excluded: chain A residue 727 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 102 THR 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 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 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 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 49 optimal weight: 0.0010 chunk 22 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3853 r_free = 0.3853 target = 0.147219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.111524 restraints weight = 15691.934| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.94 r_work: 0.3218 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10814 Z= 0.120 Angle : 0.580 9.528 14665 Z= 0.283 Chirality : 0.044 0.344 1600 Planarity : 0.004 0.064 1877 Dihedral : 8.920 107.951 1599 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.84 % Allowed : 28.87 % Favored : 66.29 % 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: -0.14 (0.24), residues: 1305 helix: 1.62 (0.28), residues: 344 sheet: -0.63 (0.35), residues: 240 loop : -0.73 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 53 TYR 0.012 0.001 TYR B 369 PHE 0.012 0.001 PHE A 795 TRP 0.011 0.001 TRP A 766 HIS 0.004 0.001 HIS B 415 Details of bonding type rmsd covalent geometry : bond 0.00273 (10778) covalent geometry : angle 0.56084 (14591) SS BOND : bond 0.00222 ( 25) SS BOND : angle 0.91984 ( 50) hydrogen bonds : bond 0.03693 ( 372) hydrogen bonds : angle 4.88046 ( 1020) metal coordination : bond 0.00073 ( 3) link_BETA1-4 : bond 0.00799 ( 1) link_BETA1-4 : angle 2.05463 ( 3) link_NAG-ASN : bond 0.00560 ( 7) link_NAG-ASN : angle 3.70070 ( 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 192 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 136 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.6189 (mmm) cc_final: 0.5541 (mmp) REVERT: A 408 TYR cc_start: 0.7492 (m-80) cc_final: 0.7284 (m-10) REVERT: A 674 CYS cc_start: 0.8513 (t) cc_final: 0.7837 (p) REVERT: A 798 TYR cc_start: 0.7404 (m-10) cc_final: 0.6664 (t80) REVERT: A 825 TYR cc_start: 0.7175 (t80) cc_final: 0.6942 (t80) REVERT: C 81 GLU cc_start: 0.8327 (pp20) cc_final: 0.7937 (pp20) REVERT: D 102 ARG cc_start: 0.8558 (ptt90) cc_final: 0.7854 (ptt90) REVERT: B 160 LYS cc_start: 0.8862 (tmtt) cc_final: 0.8516 (mptt) REVERT: B 375 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8506 (mtpt) REVERT: B 487 GLU cc_start: 0.8593 (pm20) cc_final: 0.7932 (pm20) REVERT: B 585 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6474 (pm20) outliers start: 56 outliers final: 41 residues processed: 185 average time/residue: 0.0952 time to fit residues: 25.6432 Evaluate side-chains 175 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 132 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 551 ASP 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 C residue 52 SER Chi-restraints excluded: chain C residue 75 ILE 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 74 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 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 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 375 LYS 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 469 CYS Chi-restraints excluded: chain B residue 508 LEU 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 582 CYS Chi-restraints excluded: chain B residue 585 GLU Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 672 ILE 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: 0.7980 chunk 72 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.146938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.112306 restraints weight = 15766.106| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.91 r_work: 0.3220 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10814 Z= 0.133 Angle : 0.570 10.272 14665 Z= 0.281 Chirality : 0.044 0.400 1600 Planarity : 0.004 0.045 1877 Dihedral : 8.342 106.031 1599 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 5.62 % Allowed : 28.18 % 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: -0.15 (0.24), residues: 1305 helix: 1.66 (0.28), residues: 344 sheet: -0.70 (0.34), residues: 246 loop : -0.74 (0.24), residues: 715 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 0.011 0.001 PHE B 235 TRP 0.011 0.001 TRP A 460 HIS 0.005 0.001 HIS B 415 Details of bonding type rmsd covalent geometry : bond 0.00306 (10778) covalent geometry : angle 0.54784 (14591) SS BOND : bond 0.00217 ( 25) SS BOND : angle 0.88948 ( 50) hydrogen bonds : bond 0.03688 ( 372) hydrogen bonds : angle 4.82187 ( 1020) metal coordination : bond 0.00025 ( 3) link_BETA1-4 : bond 0.00830 ( 1) link_BETA1-4 : angle 1.95762 ( 3) link_NAG-ASN : bond 0.01034 ( 7) link_NAG-ASN : angle 3.97915 ( 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 196 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 131 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.6386 (mmm) cc_final: 0.5748 (mmp) REVERT: A 674 CYS cc_start: 0.8578 (t) cc_final: 0.7898 (p) REVERT: A 798 TYR cc_start: 0.7329 (m-10) cc_final: 0.6661 (t80) REVERT: A 825 TYR cc_start: 0.7272 (t80) cc_final: 0.7018 (t80) REVERT: C 81 GLU cc_start: 0.8350 (pp20) cc_final: 0.7953 (pp20) REVERT: B 160 LYS cc_start: 0.8924 (tmtt) cc_final: 0.8598 (mptt) REVERT: B 375 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8513 (mtpt) REVERT: B 487 GLU cc_start: 0.8675 (pm20) cc_final: 0.7887 (pm20) REVERT: B 585 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6407 (pm20) outliers start: 65 outliers final: 57 residues processed: 184 average time/residue: 0.0858 time to fit residues: 23.8112 Evaluate side-chains 183 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 124 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 544 PHE Chi-restraints excluded: chain A residue 551 ASP 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 722 SER 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 51 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 74 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 62 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 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 375 LYS 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 507 THR Chi-restraints excluded: chain B residue 508 LEU 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 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: 5.9990 chunk 40 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 123 optimal weight: 0.0040 chunk 128 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 22 optimal weight: 0.2980 chunk 127 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.146407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.105879 restraints weight = 15927.905| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.03 r_work: 0.3202 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1645 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= 0.129 Angle : 0.572 7.945 14665 Z= 0.283 Chirality : 0.043 0.220 1600 Planarity : 0.004 0.055 1877 Dihedral : 9.679 123.638 1599 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 6.48 % Allowed : 27.66 % Favored : 65.86 % 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: -0.09 (0.24), residues: 1305 helix: 1.71 (0.28), residues: 344 sheet: -0.62 (0.35), residues: 240 loop : -0.72 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 53 TYR 0.014 0.001 TYR A 384 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 covalent geometry : bond 0.00294 (10778) covalent geometry : angle 0.55765 (14591) SS BOND : bond 0.00206 ( 25) SS BOND : angle 0.84816 ( 50) hydrogen bonds : bond 0.03610 ( 372) hydrogen bonds : angle 4.75500 ( 1020) metal coordination : bond 0.00007 ( 3) link_BETA1-4 : bond 0.00815 ( 1) link_BETA1-4 : angle 1.87799 ( 3) link_NAG-ASN : bond 0.00559 ( 7) link_NAG-ASN : angle 3.20831 ( 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 206 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 131 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.6220 (mmm) cc_final: 0.5623 (mmp) REVERT: A 674 CYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7699 (p) REVERT: A 798 TYR cc_start: 0.7367 (m-10) cc_final: 0.6636 (t80) REVERT: A 825 TYR cc_start: 0.7040 (t80) cc_final: 0.6799 (t80) REVERT: C 81 GLU cc_start: 0.8371 (pp20) cc_final: 0.7964 (pp20) REVERT: B 160 LYS cc_start: 0.8776 (tmtt) cc_final: 0.8369 (mptt) REVERT: B 375 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8416 (mtpt) REVERT: B 487 GLU cc_start: 0.8607 (pm20) cc_final: 0.7777 (pm20) REVERT: B 585 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6391 (pm20) outliers start: 75 outliers final: 61 residues processed: 192 average time/residue: 0.0866 time to fit residues: 25.1576 Evaluate side-chains 192 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 128 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 505 ASN Chi-restraints excluded: chain A residue 551 ASP 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 787 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 74 ASN 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 62 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 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 348 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 375 LYS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 23 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3830 r_free = 0.3830 target = 0.144639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.103982 restraints weight = 15901.171| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.04 r_work: 0.3189 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1716 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= 0.167 Angle : 0.595 8.094 14665 Z= 0.296 Chirality : 0.043 0.208 1600 Planarity : 0.004 0.043 1877 Dihedral : 9.469 121.657 1599 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 6.66 % Allowed : 26.79 % Favored : 66.55 % 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: -0.20 (0.24), residues: 1305 helix: 1.65 (0.28), residues: 345 sheet: -0.71 (0.35), residues: 244 loop : -0.79 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 53 TYR 0.017 0.001 TYR B 369 PHE 0.014 0.001 PHE B 235 TRP 0.012 0.001 TRP A 460 HIS 0.006 0.001 HIS B 415 Details of bonding type rmsd covalent geometry : bond 0.00393 (10778) covalent geometry : angle 0.57890 (14591) SS BOND : bond 0.00307 ( 25) SS BOND : angle 0.94175 ( 50) hydrogen bonds : bond 0.03802 ( 372) hydrogen bonds : angle 4.80871 ( 1020) metal coordination : bond 0.00076 ( 3) link_BETA1-4 : bond 0.00909 ( 1) link_BETA1-4 : angle 1.83425 ( 3) link_NAG-ASN : bond 0.00498 ( 7) link_NAG-ASN : angle 3.47048 ( 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 205 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 128 time to evaluate : 0.407 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: 0.6310 (mmm) cc_final: 0.5743 (mmp) REVERT: A 674 CYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7709 (p) REVERT: A 798 TYR cc_start: 0.7355 (m-10) cc_final: 0.6643 (t80) REVERT: A 825 TYR cc_start: 0.7043 (t80) cc_final: 0.6792 (t80) REVERT: C 81 GLU cc_start: 0.8427 (pp20) cc_final: 0.7984 (pp20) REVERT: B 160 LYS cc_start: 0.8787 (tmtt) cc_final: 0.8373 (mptt) REVERT: B 375 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8420 (mtpt) REVERT: B 487 GLU cc_start: 0.8573 (pm20) cc_final: 0.7727 (pm20) REVERT: B 494 MET cc_start: 0.8841 (ptp) cc_final: 0.8624 (ptm) REVERT: B 532 LYS cc_start: 0.7514 (ttmt) cc_final: 0.7213 (ttmt) REVERT: B 585 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.6288 (pm20) outliers start: 77 outliers final: 67 residues processed: 191 average time/residue: 0.0877 time to fit residues: 25.5540 Evaluate side-chains 194 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 124 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 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 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 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 74 ASN 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 62 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 330 SER 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 375 LYS 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 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 Chi-restraints excluded: chain B residue 680 SER 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: 0.8980 chunk 39 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 124 optimal weight: 0.3980 chunk 105 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3854 r_free = 0.3854 target = 0.146630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.106092 restraints weight = 15914.303| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.07 r_work: 0.3211 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10814 Z= 0.120 Angle : 0.574 8.470 14665 Z= 0.283 Chirality : 0.042 0.202 1600 Planarity : 0.004 0.051 1877 Dihedral : 9.088 120.927 1599 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 5.62 % Allowed : 27.83 % Favored : 66.55 % 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: 1.74 (0.28), residues: 345 sheet: -0.56 (0.36), residues: 233 loop : -0.75 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 53 TYR 0.013 0.001 TYR B 369 PHE 0.016 0.001 PHE A 795 TRP 0.011 0.001 TRP D 47 HIS 0.005 0.001 HIS B 415 Details of bonding type rmsd covalent geometry : bond 0.00277 (10778) covalent geometry : angle 0.55637 (14591) SS BOND : bond 0.00202 ( 25) SS BOND : angle 0.84781 ( 50) hydrogen bonds : bond 0.03547 ( 372) hydrogen bonds : angle 4.70641 ( 1020) metal coordination : bond 0.00040 ( 3) link_BETA1-4 : bond 0.01005 ( 1) link_BETA1-4 : angle 1.91696 ( 3) link_NAG-ASN : bond 0.00573 ( 7) link_NAG-ASN : angle 3.55802 ( 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 188 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 123 time to evaluate : 0.411 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: 0.6272 (mmm) cc_final: 0.5724 (mmp) REVERT: A 674 CYS cc_start: 0.8323 (t) cc_final: 0.7671 (p) REVERT: A 798 TYR cc_start: 0.7314 (m-10) cc_final: 0.6625 (t80) REVERT: C 53 ARG cc_start: 0.7239 (ttm110) cc_final: 0.6516 (mtp180) REVERT: C 81 GLU cc_start: 0.8416 (pp20) cc_final: 0.8003 (pp20) REVERT: D 76 LYS cc_start: 0.8759 (mtmm) cc_final: 0.8520 (mtmm) REVERT: B 160 LYS cc_start: 0.8753 (tmtt) cc_final: 0.8360 (mptt) REVERT: B 375 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8417 (mtpt) REVERT: B 487 GLU cc_start: 0.8586 (pm20) cc_final: 0.7726 (pm20) REVERT: B 494 MET cc_start: 0.8783 (ptp) cc_final: 0.8507 (ptm) REVERT: B 495 TYR cc_start: 0.7895 (m-10) cc_final: 0.7501 (m-10) REVERT: B 532 LYS cc_start: 0.7467 (ttmt) cc_final: 0.7267 (ttmt) REVERT: B 585 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6368 (pm20) outliers start: 65 outliers final: 59 residues processed: 177 average time/residue: 0.0847 time to fit residues: 22.8578 Evaluate side-chains 183 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 122 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 662 LEU Chi-restraints excluded: chain A residue 683 LEU 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 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 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 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 330 SER 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 375 LYS 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 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 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: 0.7980 chunk 19 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 111 optimal weight: 0.2980 chunk 117 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.146576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.108247 restraints weight = 15807.129| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.06 r_work: 0.3213 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1862 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= 0.127 Angle : 0.576 8.653 14665 Z= 0.285 Chirality : 0.042 0.198 1600 Planarity : 0.004 0.055 1877 Dihedral : 8.786 120.889 1599 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 5.45 % Allowed : 28.09 % 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: -0.04 (0.24), residues: 1305 helix: 1.77 (0.28), residues: 345 sheet: -0.53 (0.36), residues: 231 loop : -0.73 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 53 TYR 0.014 0.001 TYR B 369 PHE 0.016 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 covalent geometry : bond 0.00294 (10778) covalent geometry : angle 0.55782 (14591) SS BOND : bond 0.00206 ( 25) SS BOND : angle 0.83926 ( 50) hydrogen bonds : bond 0.03552 ( 372) hydrogen bonds : angle 4.67712 ( 1020) metal coordination : bond 0.00026 ( 3) link_BETA1-4 : bond 0.01063 ( 1) link_BETA1-4 : angle 1.97490 ( 3) link_NAG-ASN : bond 0.00555 ( 7) link_NAG-ASN : angle 3.64269 ( 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 185 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 122 time to evaluate : 0.434 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: 0.6311 (mmm) cc_final: 0.5781 (mmp) REVERT: A 507 ARG cc_start: 0.6251 (ptp-170) cc_final: 0.6015 (ptt-90) REVERT: A 674 CYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7635 (p) REVERT: A 798 TYR cc_start: 0.7313 (m-10) cc_final: 0.6636 (t80) REVERT: C 3 GLN cc_start: 0.8039 (mp10) cc_final: 0.7666 (mp10) REVERT: C 53 ARG cc_start: 0.7209 (ttm110) cc_final: 0.6492 (mtp180) REVERT: C 81 GLU cc_start: 0.8423 (pp20) cc_final: 0.8032 (pp20) REVERT: D 76 LYS cc_start: 0.8720 (mtmm) cc_final: 0.8479 (mtmm) REVERT: B 160 LYS cc_start: 0.8708 (tmtt) cc_final: 0.8316 (mptt) REVERT: B 375 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8381 (mtpt) REVERT: B 487 GLU cc_start: 0.8592 (pm20) cc_final: 0.7731 (pm20) REVERT: B 494 MET cc_start: 0.8760 (ptp) cc_final: 0.8475 (ptp) REVERT: B 495 TYR cc_start: 0.7907 (m-10) cc_final: 0.7556 (m-10) REVERT: B 585 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.6343 (pm20) outliers start: 63 outliers final: 59 residues processed: 172 average time/residue: 0.0938 time to fit residues: 23.6887 Evaluate side-chains 183 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 121 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 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 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 A residue 818 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 25 SER 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 91 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 62 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 375 LYS 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 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 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: 0.1980 chunk 1 optimal weight: 0.0050 chunk 32 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 chunk 46 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.149316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.111474 restraints weight = 15917.050| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.08 r_work: 0.3259 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10814 Z= 0.098 Angle : 0.560 8.969 14665 Z= 0.275 Chirality : 0.041 0.189 1600 Planarity : 0.004 0.053 1877 Dihedral : 8.378 119.908 1599 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.49 % Allowed : 29.39 % 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: 0.08 (0.24), residues: 1305 helix: 1.90 (0.29), residues: 344 sheet: -0.38 (0.36), residues: 229 loop : -0.70 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 53 TYR 0.011 0.001 TYR A 789 PHE 0.017 0.001 PHE A 795 TRP 0.012 0.001 TRP D 47 HIS 0.004 0.001 HIS B 415 Details of bonding type rmsd covalent geometry : bond 0.00216 (10778) covalent geometry : angle 0.54070 (14591) SS BOND : bond 0.00166 ( 25) SS BOND : angle 0.76666 ( 50) hydrogen bonds : bond 0.03275 ( 372) hydrogen bonds : angle 4.56547 ( 1020) metal coordination : bond 0.00156 ( 3) link_BETA1-4 : bond 0.01096 ( 1) link_BETA1-4 : angle 1.96127 ( 3) link_NAG-ASN : bond 0.00630 ( 7) link_NAG-ASN : angle 3.76752 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2820.70 seconds wall clock time: 49 minutes 9.51 seconds (2949.51 seconds total)