Starting phenix.real_space_refine on Sun May 3 03:52:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xy4_72322/05_2026/9xy4_72322_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xy4_72322/05_2026/9xy4_72322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xy4_72322/05_2026/9xy4_72322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xy4_72322/05_2026/9xy4_72322.map" model { file = "/net/cci-nas-00/data/ceres_data/9xy4_72322/05_2026/9xy4_72322_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xy4_72322/05_2026/9xy4_72322_neut.cif" } resolution = 3.12 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= 0.007 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 78 5.16 5 C 6473 2.51 5 N 1732 2.21 5 O 1938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 10223 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3424 Classifications: {'peptide': 426} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 401} 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: 2.52, per 1000 atoms: 0.25 Number of scatterers: 10223 At special positions: 0 Unit cell: (92.66, 111.52, 168.92, 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 78 16.00 O 1938 8.00 N 1732 7.00 C 6473 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=2.02 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=2.03 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: 0.99 Conformation dependent library (CDL) restraints added in 377.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 702 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 415 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 405 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 409 " 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2380 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 17 sheets defined 31.4% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 404 through 425 Processing helix chain 'A' and resid 464 through 471 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 628 through 632 Processing helix chain 'A' and resid 633 through 639 removed outlier: 4.133A pdb=" N ASP A 637 " --> pdb=" O HIS A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 660 through 662 No H-bonds generated for 'chain 'A' and resid 660 through 662' Processing helix chain 'A' and resid 665 through 688 removed outlier: 4.371A pdb=" N ARG A 681 " --> pdb=" O MET A 677 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP A 682 " --> pdb=" O THR A 678 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 685 " --> pdb=" O ARG A 681 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 711 removed outlier: 3.515A pdb=" N SER A 699 " --> pdb=" O ILE A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 737 removed outlier: 3.544A pdb=" N PHE A 731 " --> pdb=" O LEU A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 762 Processing helix chain 'A' and resid 768 through 787 Processing helix chain 'A' and resid 793 through 823 removed outlier: 4.730A pdb=" N GLN A 808 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL A 809 " --> pdb=" O ILE A 805 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.691A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.766A pdb=" N THR D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 90 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 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 243 through 265 removed outlier: 3.507A pdb=" N THR B 247 " --> pdb=" O GLU B 243 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN B 264 " --> pdb=" O ASP B 260 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR B 265 " --> pdb=" O ILE B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 325 Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 343 through 347 removed outlier: 3.659A pdb=" N GLY B 346 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR B 347 " --> pdb=" O ASP B 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 343 through 347' Processing helix chain 'B' and resid 395 through 412 Processing helix chain 'B' and resid 444 through 448 removed outlier: 3.694A pdb=" N ASN B 447 " --> pdb=" O HIS B 444 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS B 448 " --> pdb=" O GLU B 445 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 444 through 448' Processing helix chain 'B' and resid 454 through 465 removed outlier: 3.504A pdb=" N ILE B 458 " --> pdb=" O SER B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 585 removed outlier: 3.582A pdb=" N ARG B 584 " --> pdb=" O PRO B 580 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU B 585 " --> pdb=" O PHE B 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 580 through 585' Processing helix chain 'B' and resid 647 through 659 Processing helix chain 'B' and resid 660 through 671 removed outlier: 3.540A pdb=" N GLY B 665 " --> pdb=" O ILE B 661 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN B 671 " --> pdb=" O PHE B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 697 removed outlier: 3.724A 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 Processing sheet with id=AA2, first strand: chain 'A' and resid 510 through 513 removed outlier: 3.553A 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 607 through 610 Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.789A pdb=" N VAL C 19 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N THR C 69 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 10.660A pdb=" N GLN C 27 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 10.141A pdb=" N SER C 67 " --> pdb=" O GLN C 27 " (cutoff:3.500A) removed outlier: 12.321A pdb=" N ILE C 29 " --> pdb=" O SER C 65 " (cutoff:3.500A) removed outlier: 12.369A pdb=" N SER C 65 " --> pdb=" O ILE C 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.853A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 6 through 7 removed outlier: 3.629A pdb=" N SER D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU D 79 " --> pdb=" O CYS D 22 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.903A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.448A pdb=" N ARG D 98 " --> pdb=" O ASP D 107 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 43 through 45 removed outlier: 7.970A pdb=" N VAL B 136 " --> pdb=" O PRO B 151 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 105 through 107 removed outlier: 4.337A pdb=" N VAL B 96 " --> pdb=" O TYR B 107 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N CYS B 225 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU B 280 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU B 227 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE B 282 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B 229 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ILE B 284 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA B 231 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N LEU B 334 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS B 226 " --> pdb=" O LEU B 334 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N HIS B 336 " --> pdb=" O LYS B 226 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU B 228 " --> pdb=" O HIS B 336 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N PHE B 338 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL B 230 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 368 through 371 removed outlier: 3.500A pdb=" N LYS B 376 " --> pdb=" O SER B 371 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AB5, first strand: chain 'B' and resid 522 through 523 Processing sheet with id=AB6, first strand: chain 'B' and resid 533 through 535 removed outlier: 6.981A pdb=" N SER B 546 " --> pdb=" O CYS B 534 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 573 through 574 Processing sheet with id=AB8, first strand: chain 'B' and resid 628 through 629 removed outlier: 3.987A pdb=" N LYS B 628 " --> pdb=" O CYS B 635 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 1035 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: 1.63 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3316 1.34 - 1.46: 2183 1.46 - 1.58: 4870 1.58 - 1.69: 0 1.69 - 1.81: 98 Bond restraints: 10467 Sorted by residual: bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C1 NAG B 705 " pdb=" O5 NAG B 705 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C1 NAG B 708 " pdb=" O5 NAG B 708 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C1 NAG B 704 " pdb=" O5 NAG B 704 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C1 NAG B 706 " pdb=" O5 NAG B 706 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.02e+01 ... (remaining 10462 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 13685 1.36 - 2.72: 415 2.72 - 4.08: 63 4.08 - 5.44: 13 5.44 - 6.80: 2 Bond angle restraints: 14178 Sorted by residual: angle pdb=" N VAL A 554 " pdb=" CA VAL A 554 " pdb=" C VAL A 554 " ideal model delta sigma weight residual 113.71 110.27 3.44 9.50e-01 1.11e+00 1.31e+01 angle pdb=" CA CYS B 506 " pdb=" CB CYS B 506 " pdb=" SG CYS B 506 " ideal model delta sigma weight residual 114.40 121.20 -6.80 2.30e+00 1.89e-01 8.73e+00 angle pdb=" CA GLY C 66 " pdb=" C GLY C 66 " pdb=" N SER C 67 " ideal model delta sigma weight residual 114.23 116.79 -2.56 8.80e-01 1.29e+00 8.48e+00 angle pdb=" N ILE A 804 " pdb=" CA ILE A 804 " pdb=" C ILE A 804 " ideal model delta sigma weight residual 113.00 109.35 3.65 1.30e+00 5.92e-01 7.88e+00 angle pdb=" N CYS B 506 " pdb=" CA CYS B 506 " pdb=" CB CYS B 506 " ideal model delta sigma weight residual 111.91 108.06 3.85 1.52e+00 4.33e-01 6.43e+00 ... (remaining 14173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.02: 6081 25.02 - 50.04: 240 50.04 - 75.07: 27 75.07 - 100.09: 32 100.09 - 125.11: 16 Dihedral angle restraints: 6396 sinusoidal: 2692 harmonic: 3704 Sorted by residual: dihedral pdb=" CA CYS B 478 " pdb=" C CYS B 478 " pdb=" N GLY B 479 " pdb=" CA GLY B 479 " ideal model delta harmonic sigma weight residual -180.00 -158.98 -21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA TRP B 312 " pdb=" C TRP B 312 " pdb=" N ASP B 313 " pdb=" CA ASP B 313 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" C2 NAG B 708 " pdb=" C1 NAG B 708 " pdb=" O5 NAG B 708 " pdb=" C5 NAG B 708 " ideal model delta sinusoidal sigma weight residual -62.96 62.15 -125.11 1 3.00e+01 1.11e-03 1.68e+01 ... (remaining 6393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1343 0.062 - 0.125: 206 0.125 - 0.187: 9 0.187 - 0.249: 0 0.249 - 0.311: 1 Chirality restraints: 1559 Sorted by residual: chirality pdb=" C4 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" C5 NAG E 1 " pdb=" O4 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.22 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.21e+00 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 -2.22 -0.18 2.00e-01 2.50e+01 8.33e-01 ... (remaining 1556 not shown) Planarity restraints: 1829 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 403 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO A 404 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 404 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 404 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 79 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO C 80 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 562 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO A 563 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 563 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 563 " -0.015 5.00e-02 4.00e+02 ... (remaining 1826 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 395 2.71 - 3.26: 10381 3.26 - 3.81: 16388 3.81 - 4.35: 20335 4.35 - 4.90: 35001 Nonbonded interactions: 82500 Sorted by model distance: nonbonded pdb=" O VAL B 477 " pdb="CA CA B 701 " model vdw 2.165 2.510 nonbonded pdb=" NH2 ARG D 67 " pdb=" OD2 ASP D 90 " model vdw 2.198 3.120 nonbonded pdb=" OD2 ASP B 490 " pdb="CA CA B 701 " model vdw 2.199 2.510 nonbonded pdb=" NH1 ARG D 38 " pdb=" OD1 ASP D 90 " model vdw 2.209 3.120 nonbonded pdb=" OG1 THR C 94 " pdb=" OD2 ASP D 59 " model vdw 2.220 3.040 ... (remaining 82495 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.000 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 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 : 0.006 0.398 10503 Z= 0.255 Angle : 0.593 9.184 14252 Z= 0.321 Chirality : 0.044 0.311 1559 Planarity : 0.004 0.038 1822 Dihedral : 16.473 125.111 3941 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.47 % Allowed : 7.56 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 0.01 (0.25), residues: 1269 helix: 2.13 (0.29), residues: 315 sheet: -0.60 (0.35), residues: 247 loop : -0.74 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 584 TYR 0.012 0.001 TYR C 49 PHE 0.015 0.001 PHE B 235 TRP 0.013 0.001 TRP B 312 HIS 0.003 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00480 (10467) covalent geometry : angle 0.57475 (14178) SS BOND : bond 0.00263 ( 25) SS BOND : angle 0.98856 ( 50) hydrogen bonds : bond 0.19301 ( 374) hydrogen bonds : angle 8.11972 ( 1035) metal coordination : bond 0.22976 ( 3) link_BETA1-4 : bond 0.01304 ( 1) link_BETA1-4 : angle 4.46959 ( 3) link_NAG-ASN : bond 0.00476 ( 7) link_NAG-ASN : angle 3.24734 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 195 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 459 PHE cc_start: 0.5828 (t80) cc_final: 0.5627 (t80) REVERT: A 546 SER cc_start: 0.7587 (m) cc_final: 0.7081 (t) REVERT: A 635 MET cc_start: 0.8286 (mmm) cc_final: 0.7906 (mmt) REVERT: A 746 ARG cc_start: 0.5995 (tpp80) cc_final: 0.5361 (ptt-90) REVERT: B 319 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7464 (tm-30) outliers start: 39 outliers final: 13 residues processed: 226 average time/residue: 0.1120 time to fit residues: 35.2467 Evaluate side-chains 134 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 107 ASP 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 247 THR Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 501 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS A 550 GLN A 583 ASN A 736 GLN C 27 GLN C 38 GLN C 89 GLN D 39 GLN B 118 HIS B 297 HIS B 341 GLN ** B 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 GLN B 475 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.145060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.103498 restraints weight = 16346.170| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.51 r_work: 0.3242 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10503 Z= 0.224 Angle : 0.670 9.443 14252 Z= 0.329 Chirality : 0.047 0.229 1559 Planarity : 0.005 0.063 1822 Dihedral : 15.766 115.094 1570 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.00 % Allowed : 12.10 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -0.03 (0.24), residues: 1269 helix: 2.01 (0.29), residues: 323 sheet: -0.79 (0.34), residues: 249 loop : -0.69 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 490 TYR 0.013 0.001 TYR D 50 PHE 0.015 0.002 PHE A 781 TRP 0.015 0.001 TRP B 312 HIS 0.004 0.001 HIS B 415 Details of bonding type rmsd covalent geometry : bond 0.00516 (10467) covalent geometry : angle 0.65316 (14178) SS BOND : bond 0.00371 ( 25) SS BOND : angle 1.02678 ( 50) hydrogen bonds : bond 0.04757 ( 374) hydrogen bonds : angle 5.97552 ( 1035) metal coordination : bond 0.01213 ( 3) link_BETA1-4 : bond 0.01886 ( 1) link_BETA1-4 : angle 2.58583 ( 3) link_NAG-ASN : bond 0.00508 ( 7) link_NAG-ASN : angle 3.67125 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 121 time to evaluate : 0.394 Fit side-chains REVERT: A 459 PHE cc_start: 0.6889 (t80) cc_final: 0.6208 (t80) REVERT: A 572 LYS cc_start: 0.9115 (tptp) cc_final: 0.8853 (mtmt) REVERT: A 635 MET cc_start: 0.8149 (mmm) cc_final: 0.7317 (mmt) REVERT: A 746 ARG cc_start: 0.5430 (tpp80) cc_final: 0.4432 (ptt-90) REVERT: D 107 ASP cc_start: 0.8667 (m-30) cc_final: 0.8465 (m-30) REVERT: B 449 MET cc_start: 0.8474 (mmt) cc_final: 0.8009 (mtt) REVERT: B 490 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7347 (t0) REVERT: B 570 LEU cc_start: 0.7633 (mt) cc_final: 0.7308 (mt) REVERT: B 581 PHE cc_start: 0.6391 (t80) cc_final: 0.6135 (t80) REVERT: B 642 GLU cc_start: 0.7230 (tp30) cc_final: 0.6721 (pp20) outliers start: 45 outliers final: 29 residues processed: 152 average time/residue: 0.0974 time to fit residues: 21.6650 Evaluate side-chains 135 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 591 ASP Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 676 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 117 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 66 optimal weight: 0.0050 chunk 8 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.147700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.106370 restraints weight = 16432.836| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 3.57 r_work: 0.3284 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10503 Z= 0.132 Angle : 0.613 10.526 14252 Z= 0.293 Chirality : 0.045 0.210 1559 Planarity : 0.004 0.060 1822 Dihedral : 14.534 115.799 1567 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.65 % Allowed : 13.97 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1269 helix: 2.13 (0.29), residues: 323 sheet: -0.66 (0.34), residues: 246 loop : -0.65 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.012 0.001 TYR D 50 PHE 0.017 0.001 PHE B 683 TRP 0.012 0.001 TRP B 312 HIS 0.003 0.001 HIS B 130 Details of bonding type rmsd covalent geometry : bond 0.00284 (10467) covalent geometry : angle 0.59289 (14178) SS BOND : bond 0.00214 ( 25) SS BOND : angle 0.68851 ( 50) hydrogen bonds : bond 0.04003 ( 374) hydrogen bonds : angle 5.39276 ( 1035) metal coordination : bond 0.00336 ( 3) link_BETA1-4 : bond 0.01778 ( 1) link_BETA1-4 : angle 2.47529 ( 3) link_NAG-ASN : bond 0.00588 ( 7) link_NAG-ASN : angle 3.91205 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 118 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 459 PHE cc_start: 0.6826 (t80) cc_final: 0.6173 (t80) REVERT: A 572 LYS cc_start: 0.9178 (tptp) cc_final: 0.8858 (mtmt) REVERT: A 635 MET cc_start: 0.8117 (mmm) cc_final: 0.7434 (mmt) REVERT: A 746 ARG cc_start: 0.5429 (tpp80) cc_final: 0.4444 (ptt-90) REVERT: B 449 MET cc_start: 0.8491 (mmt) cc_final: 0.7992 (mtt) REVERT: B 490 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7060 (t0) REVERT: B 584 ARG cc_start: 0.6738 (mtp-110) cc_final: 0.6355 (mtp-110) REVERT: B 642 GLU cc_start: 0.7273 (tp30) cc_final: 0.6749 (pp20) outliers start: 41 outliers final: 29 residues processed: 144 average time/residue: 0.0854 time to fit residues: 18.3637 Evaluate side-chains 139 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 591 ASP Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 676 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 81 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 20 optimal weight: 0.0970 chunk 5 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.146766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.106105 restraints weight = 16427.177| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.52 r_work: 0.3288 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10503 Z= 0.126 Angle : 0.583 9.168 14252 Z= 0.280 Chirality : 0.044 0.217 1559 Planarity : 0.004 0.061 1822 Dihedral : 13.099 112.043 1565 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.83 % Allowed : 15.39 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.24), residues: 1269 helix: 2.18 (0.29), residues: 323 sheet: -0.55 (0.35), residues: 236 loop : -0.62 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.011 0.001 TYR B 369 PHE 0.012 0.001 PHE B 527 TRP 0.011 0.001 TRP B 312 HIS 0.002 0.000 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00283 (10467) covalent geometry : angle 0.57059 (14178) SS BOND : bond 0.00198 ( 25) SS BOND : angle 0.69833 ( 50) hydrogen bonds : bond 0.03680 ( 374) hydrogen bonds : angle 5.07713 ( 1035) metal coordination : bond 0.00335 ( 3) link_BETA1-4 : bond 0.01689 ( 1) link_BETA1-4 : angle 2.73887 ( 3) link_NAG-ASN : bond 0.00612 ( 7) link_NAG-ASN : angle 2.94847 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 116 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 459 PHE cc_start: 0.6857 (t80) cc_final: 0.6179 (t80) REVERT: A 572 LYS cc_start: 0.9248 (tptp) cc_final: 0.8895 (mtmt) REVERT: A 746 ARG cc_start: 0.5514 (tpp80) cc_final: 0.4476 (ptt-90) REVERT: C 42 LYS cc_start: 0.7604 (mmmt) cc_final: 0.6825 (mtpt) REVERT: B 449 MET cc_start: 0.8519 (mmt) cc_final: 0.7999 (mtt) REVERT: B 490 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7003 (t0) REVERT: B 584 ARG cc_start: 0.6776 (mtp-110) cc_final: 0.6481 (mtp-110) REVERT: B 642 GLU cc_start: 0.7306 (tp30) cc_final: 0.6818 (pp20) outliers start: 43 outliers final: 30 residues processed: 147 average time/residue: 0.0895 time to fit residues: 19.7350 Evaluate side-chains 137 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 591 ASP Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 792 PHE Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 671 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 34 optimal weight: 0.1980 chunk 59 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.147499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.106531 restraints weight = 16421.563| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.54 r_work: 0.3285 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10503 Z= 0.129 Angle : 0.597 9.880 14252 Z= 0.282 Chirality : 0.044 0.192 1559 Planarity : 0.004 0.063 1822 Dihedral : 12.818 110.911 1565 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.74 % Allowed : 16.01 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1269 helix: 2.13 (0.29), residues: 326 sheet: -0.58 (0.35), residues: 237 loop : -0.62 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 72 TYR 0.010 0.001 TYR B 369 PHE 0.018 0.001 PHE B 527 TRP 0.011 0.001 TRP B 312 HIS 0.002 0.000 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00293 (10467) covalent geometry : angle 0.58387 (14178) SS BOND : bond 0.00252 ( 25) SS BOND : angle 0.73431 ( 50) hydrogen bonds : bond 0.03528 ( 374) hydrogen bonds : angle 4.95630 ( 1035) metal coordination : bond 0.00307 ( 3) link_BETA1-4 : bond 0.01576 ( 1) link_BETA1-4 : angle 3.12406 ( 3) link_NAG-ASN : bond 0.00550 ( 7) link_NAG-ASN : angle 2.94615 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 114 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 459 PHE cc_start: 0.6872 (t80) cc_final: 0.6185 (t80) REVERT: A 572 LYS cc_start: 0.9255 (tptp) cc_final: 0.8876 (mtmt) REVERT: A 714 ARG cc_start: 0.7513 (tpp-160) cc_final: 0.6948 (tpp80) REVERT: A 746 ARG cc_start: 0.5488 (tpp80) cc_final: 0.4443 (ptt-90) REVERT: C 42 LYS cc_start: 0.7512 (mmmt) cc_final: 0.6703 (mtpt) REVERT: D 80 TYR cc_start: 0.8872 (m-80) cc_final: 0.8648 (m-80) REVERT: B 449 MET cc_start: 0.8475 (mmt) cc_final: 0.7929 (mtt) REVERT: B 642 GLU cc_start: 0.7353 (tp30) cc_final: 0.6825 (pp20) REVERT: B 646 GLN cc_start: 0.6871 (tp-100) cc_final: 0.6504 (tp-100) outliers start: 42 outliers final: 34 residues processed: 142 average time/residue: 0.0897 time to fit residues: 18.9746 Evaluate side-chains 139 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 591 ASP Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 792 PHE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 676 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 50 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.148040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.106761 restraints weight = 16465.294| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.56 r_work: 0.3281 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10503 Z= 0.134 Angle : 0.594 9.179 14252 Z= 0.283 Chirality : 0.044 0.202 1559 Planarity : 0.004 0.067 1822 Dihedral : 12.389 109.535 1565 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.47 % Allowed : 16.46 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1269 helix: 2.19 (0.29), residues: 326 sheet: -0.64 (0.34), residues: 247 loop : -0.55 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 24 TYR 0.010 0.001 TYR B 369 PHE 0.029 0.001 PHE B 581 TRP 0.011 0.001 TRP B 312 HIS 0.002 0.000 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00306 (10467) covalent geometry : angle 0.58079 (14178) SS BOND : bond 0.00216 ( 25) SS BOND : angle 0.78795 ( 50) hydrogen bonds : bond 0.03465 ( 374) hydrogen bonds : angle 4.85441 ( 1035) metal coordination : bond 0.00267 ( 3) link_BETA1-4 : bond 0.01407 ( 1) link_BETA1-4 : angle 3.51801 ( 3) link_NAG-ASN : bond 0.00517 ( 7) link_NAG-ASN : angle 2.87633 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 459 PHE cc_start: 0.6877 (t80) cc_final: 0.6205 (t80) REVERT: A 572 LYS cc_start: 0.9318 (tptp) cc_final: 0.8917 (mtmt) REVERT: A 714 ARG cc_start: 0.7614 (tpp-160) cc_final: 0.7026 (tpp80) REVERT: A 746 ARG cc_start: 0.5573 (tpp80) cc_final: 0.4498 (ptt180) REVERT: C 4 MET cc_start: 0.8558 (mtp) cc_final: 0.7692 (mtp) REVERT: C 42 LYS cc_start: 0.7563 (mmmt) cc_final: 0.6739 (mtpt) REVERT: B 449 MET cc_start: 0.8469 (mmt) cc_final: 0.7942 (mtt) REVERT: B 490 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7149 (t0) REVERT: B 642 GLU cc_start: 0.7380 (tp30) cc_final: 0.6851 (pp20) REVERT: B 646 GLN cc_start: 0.6925 (tp-100) cc_final: 0.6544 (tp-100) outliers start: 39 outliers final: 32 residues processed: 136 average time/residue: 0.0875 time to fit residues: 17.7910 Evaluate side-chains 136 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 591 ASP Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 792 PHE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 676 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 9 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 117 optimal weight: 0.1980 chunk 112 optimal weight: 0.0020 chunk 17 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 123 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.148679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.108523 restraints weight = 16349.960| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.53 r_work: 0.3314 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10503 Z= 0.105 Angle : 0.578 9.297 14252 Z= 0.273 Chirality : 0.043 0.193 1559 Planarity : 0.004 0.066 1822 Dihedral : 11.797 107.597 1563 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.02 % Allowed : 16.81 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 0.34 (0.24), residues: 1269 helix: 2.33 (0.29), residues: 327 sheet: -0.53 (0.35), residues: 236 loop : -0.50 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 24 TYR 0.011 0.001 TYR B 369 PHE 0.019 0.001 PHE B 581 TRP 0.011 0.001 TRP B 312 HIS 0.002 0.000 HIS B 130 Details of bonding type rmsd covalent geometry : bond 0.00229 (10467) covalent geometry : angle 0.56390 (14178) SS BOND : bond 0.00180 ( 25) SS BOND : angle 0.65538 ( 50) hydrogen bonds : bond 0.03228 ( 374) hydrogen bonds : angle 4.72967 ( 1035) metal coordination : bond 0.00117 ( 3) link_BETA1-4 : bond 0.01145 ( 1) link_BETA1-4 : angle 3.78031 ( 3) link_NAG-ASN : bond 0.00533 ( 7) link_NAG-ASN : angle 2.93531 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 0.394 Fit side-chains REVERT: A 459 PHE cc_start: 0.6857 (t80) cc_final: 0.6182 (t80) REVERT: A 572 LYS cc_start: 0.9302 (tptp) cc_final: 0.8909 (mtmt) REVERT: A 746 ARG cc_start: 0.5564 (tpp80) cc_final: 0.4479 (ptt-90) REVERT: A 786 PHE cc_start: 0.6756 (m-80) cc_final: 0.6434 (m-80) REVERT: C 4 MET cc_start: 0.8511 (mtp) cc_final: 0.7599 (mtp) REVERT: C 42 LYS cc_start: 0.7468 (mmmt) cc_final: 0.6641 (mtpt) REVERT: D 73 ASP cc_start: 0.8546 (t0) cc_final: 0.7983 (t0) REVERT: D 80 TYR cc_start: 0.8774 (m-80) cc_final: 0.8572 (m-80) REVERT: B 449 MET cc_start: 0.8424 (mmt) cc_final: 0.7873 (mtt) REVERT: B 490 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7265 (t0) REVERT: B 642 GLU cc_start: 0.7433 (tp30) cc_final: 0.6895 (pp20) outliers start: 34 outliers final: 26 residues processed: 136 average time/residue: 0.0923 time to fit residues: 18.5038 Evaluate side-chains 132 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 792 PHE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain B residue 84 THR 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 136 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 547 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 59 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 123 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 100 optimal weight: 0.1980 chunk 18 optimal weight: 0.0970 chunk 34 optimal weight: 0.4980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.149715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.108935 restraints weight = 16369.424| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.55 r_work: 0.3323 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10503 Z= 0.106 Angle : 0.589 14.634 14252 Z= 0.275 Chirality : 0.043 0.193 1559 Planarity : 0.004 0.067 1822 Dihedral : 11.436 107.016 1562 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.11 % Allowed : 17.08 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 0.38 (0.24), residues: 1269 helix: 2.34 (0.29), residues: 327 sheet: -0.47 (0.35), residues: 236 loop : -0.47 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 24 TYR 0.010 0.001 TYR B 369 PHE 0.023 0.001 PHE B 581 TRP 0.010 0.001 TRP B 312 HIS 0.002 0.000 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00235 (10467) covalent geometry : angle 0.57492 (14178) SS BOND : bond 0.00153 ( 25) SS BOND : angle 0.64903 ( 50) hydrogen bonds : bond 0.03155 ( 374) hydrogen bonds : angle 4.68648 ( 1035) metal coordination : bond 0.00138 ( 3) link_BETA1-4 : bond 0.01053 ( 1) link_BETA1-4 : angle 3.64723 ( 3) link_NAG-ASN : bond 0.00510 ( 7) link_NAG-ASN : angle 2.99875 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 543 GLN cc_start: 0.8277 (mp10) cc_final: 0.8045 (mp10) REVERT: A 572 LYS cc_start: 0.9316 (tptp) cc_final: 0.8919 (mtmt) REVERT: A 678 THR cc_start: 0.7808 (t) cc_final: 0.7601 (t) REVERT: A 746 ARG cc_start: 0.5591 (tpp80) cc_final: 0.4498 (ptt-90) REVERT: A 786 PHE cc_start: 0.6685 (m-80) cc_final: 0.6361 (m-80) REVERT: C 4 MET cc_start: 0.8527 (mtp) cc_final: 0.7585 (mtp) REVERT: C 42 LYS cc_start: 0.7463 (mmmt) cc_final: 0.6651 (mtpt) REVERT: D 73 ASP cc_start: 0.8650 (t0) cc_final: 0.8150 (t0) REVERT: B 449 MET cc_start: 0.8421 (mmt) cc_final: 0.7900 (mtt) REVERT: B 490 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7319 (t0) REVERT: B 642 GLU cc_start: 0.7464 (tp30) cc_final: 0.6955 (tm-30) outliers start: 35 outliers final: 31 residues processed: 133 average time/residue: 0.0917 time to fit residues: 18.1569 Evaluate side-chains 138 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 792 PHE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain B residue 84 THR 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 136 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 671 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 81 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 92 optimal weight: 0.4980 chunk 38 optimal weight: 0.0770 chunk 35 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.148878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.107886 restraints weight = 16323.253| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.54 r_work: 0.3295 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10503 Z= 0.120 Angle : 0.592 13.612 14252 Z= 0.277 Chirality : 0.043 0.194 1559 Planarity : 0.004 0.069 1822 Dihedral : 11.083 106.598 1562 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.02 % Allowed : 17.17 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 0.40 (0.25), residues: 1269 helix: 2.39 (0.29), residues: 326 sheet: -0.51 (0.35), residues: 246 loop : -0.44 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 24 TYR 0.009 0.001 TYR B 369 PHE 0.020 0.001 PHE B 581 TRP 0.011 0.001 TRP A 745 HIS 0.002 0.000 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00272 (10467) covalent geometry : angle 0.57708 (14178) SS BOND : bond 0.00181 ( 25) SS BOND : angle 0.71943 ( 50) hydrogen bonds : bond 0.03200 ( 374) hydrogen bonds : angle 4.68210 ( 1035) metal coordination : bond 0.00201 ( 3) link_BETA1-4 : bond 0.01169 ( 1) link_BETA1-4 : angle 3.48962 ( 3) link_NAG-ASN : bond 0.00492 ( 7) link_NAG-ASN : angle 3.12751 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.373 Fit side-chains REVERT: A 459 PHE cc_start: 0.6897 (t80) cc_final: 0.6202 (t80) REVERT: A 543 GLN cc_start: 0.8256 (mp10) cc_final: 0.8010 (mp10) REVERT: A 572 LYS cc_start: 0.9357 (tptp) cc_final: 0.8935 (mtmt) REVERT: A 678 THR cc_start: 0.7737 (t) cc_final: 0.7511 (t) REVERT: A 746 ARG cc_start: 0.5520 (tpp80) cc_final: 0.4430 (ptt-90) REVERT: A 786 PHE cc_start: 0.6688 (m-80) cc_final: 0.6386 (m-80) REVERT: C 4 MET cc_start: 0.8525 (mtp) cc_final: 0.7571 (mtp) REVERT: C 42 LYS cc_start: 0.7475 (mmmt) cc_final: 0.6674 (mtpt) REVERT: D 73 ASP cc_start: 0.8640 (t0) cc_final: 0.8137 (t0) REVERT: B 449 MET cc_start: 0.8404 (mmt) cc_final: 0.7886 (mtt) REVERT: B 490 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7210 (t0) REVERT: B 642 GLU cc_start: 0.7440 (tp30) cc_final: 0.6826 (tm-30) REVERT: B 646 GLN cc_start: 0.6937 (tp-100) cc_final: 0.6451 (tp-100) outliers start: 34 outliers final: 30 residues processed: 135 average time/residue: 0.0868 time to fit residues: 17.8185 Evaluate side-chains 139 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 792 PHE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain B residue 84 THR 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 136 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 671 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 3 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.148460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.107491 restraints weight = 16226.757| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 3.52 r_work: 0.3302 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10503 Z= 0.128 Angle : 0.601 14.747 14252 Z= 0.282 Chirality : 0.044 0.195 1559 Planarity : 0.004 0.071 1822 Dihedral : 10.741 105.953 1562 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.02 % Allowed : 17.17 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.24), residues: 1269 helix: 2.44 (0.29), residues: 326 sheet: -0.46 (0.35), residues: 236 loop : -0.45 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 24 TYR 0.010 0.001 TYR B 369 PHE 0.023 0.001 PHE B 581 TRP 0.010 0.001 TRP B 312 HIS 0.002 0.000 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00292 (10467) covalent geometry : angle 0.58510 (14178) SS BOND : bond 0.00199 ( 25) SS BOND : angle 0.76288 ( 50) hydrogen bonds : bond 0.03229 ( 374) hydrogen bonds : angle 4.67800 ( 1035) metal coordination : bond 0.00224 ( 3) link_BETA1-4 : bond 0.00758 ( 1) link_BETA1-4 : angle 3.44645 ( 3) link_NAG-ASN : bond 0.00478 ( 7) link_NAG-ASN : angle 3.24729 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 0.410 Fit side-chains REVERT: A 459 PHE cc_start: 0.6924 (t80) cc_final: 0.6284 (t80) REVERT: A 543 GLN cc_start: 0.8332 (mp10) cc_final: 0.8108 (mp10) REVERT: A 572 LYS cc_start: 0.9358 (tptp) cc_final: 0.8961 (mtmt) REVERT: A 678 THR cc_start: 0.7790 (t) cc_final: 0.7568 (t) REVERT: A 746 ARG cc_start: 0.5564 (tpp80) cc_final: 0.4421 (ptt-90) REVERT: A 784 PHE cc_start: 0.7691 (m-80) cc_final: 0.7319 (m-80) REVERT: A 786 PHE cc_start: 0.6669 (m-80) cc_final: 0.6373 (m-80) REVERT: C 4 MET cc_start: 0.8535 (mtp) cc_final: 0.7669 (mtp) REVERT: C 42 LYS cc_start: 0.7550 (mmmt) cc_final: 0.6742 (mtpt) REVERT: D 73 ASP cc_start: 0.8708 (t0) cc_final: 0.8209 (t0) REVERT: B 449 MET cc_start: 0.8412 (mmt) cc_final: 0.7943 (mtt) REVERT: B 490 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7215 (t0) REVERT: B 560 ASN cc_start: 0.7453 (OUTLIER) cc_final: 0.7150 (m-40) REVERT: B 642 GLU cc_start: 0.7447 (tp30) cc_final: 0.6861 (tm-30) REVERT: B 646 GLN cc_start: 0.6953 (tp-100) cc_final: 0.6453 (tp-100) outliers start: 34 outliers final: 32 residues processed: 137 average time/residue: 0.0906 time to fit residues: 18.4582 Evaluate side-chains 144 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 792 PHE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain B residue 84 THR 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 136 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 676 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 62 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 66 optimal weight: 0.0970 chunk 58 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.147247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.106308 restraints weight = 16563.955| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.57 r_work: 0.3280 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10503 Z= 0.133 Angle : 0.601 14.506 14252 Z= 0.282 Chirality : 0.044 0.196 1559 Planarity : 0.004 0.071 1822 Dihedral : 10.518 105.830 1562 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.85 % Allowed : 17.44 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 0.41 (0.25), residues: 1269 helix: 2.42 (0.29), residues: 326 sheet: -0.54 (0.34), residues: 246 loop : -0.44 (0.25), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 24 TYR 0.010 0.001 TYR B 369 PHE 0.022 0.001 PHE B 581 TRP 0.010 0.001 TRP A 745 HIS 0.002 0.000 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00307 (10467) covalent geometry : angle 0.58449 (14178) SS BOND : bond 0.00211 ( 25) SS BOND : angle 0.77343 ( 50) hydrogen bonds : bond 0.03258 ( 374) hydrogen bonds : angle 4.67690 ( 1035) metal coordination : bond 0.00245 ( 3) link_BETA1-4 : bond 0.00739 ( 1) link_BETA1-4 : angle 3.28201 ( 3) link_NAG-ASN : bond 0.00473 ( 7) link_NAG-ASN : angle 3.34629 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2809.01 seconds wall clock time: 48 minutes 52.92 seconds (2932.92 seconds total)