Starting phenix.real_space_refine on Thu Jul 2 22:05:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xy4_72322/07_2026/9xy4_72322_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xy4_72322/07_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_72322/07_2026/9xy4_72322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xy4_72322/07_2026/9xy4_72322.map" model { file = "/net/cci-nas-00/data/ceres_data/9xy4_72322/07_2026/9xy4_72322_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xy4_72322/07_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-dev-6108/lib/python3.11/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, 85 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.95, per 1000 atoms: 0.19 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: 0.71 Conformation dependent library (CDL) restraints added in 274.0 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: 0.20 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: 1.69 Time building geometry restraints manager: 0.93 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 3.250 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 3.250 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: 7.740 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.810 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 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/Z covalent geometry : bond 0.00480 / 0.22 (10467) covalent geometry : angle 0.57475 / 0.32 (14178) SS BOND : bond 0.00263 / 0.17 ( 25) SS BOND : angle 0.98856 / 0.80 ( 50) hydrogen bonds : bond 0.19301 / 12.97 ( 374) hydrogen bonds : angle 8.11972 / 5.94 ( 1035) metal coordination : bond 0.22976 / 11.49 ( 3) link_BETA1-4 : bond 0.01304 / 0.69 ( 1) link_BETA1-4 : angle 4.46959 / 2.37 ( 3) link_NAG-ASN : bond 0.00476 / 0.33 ( 7) link_NAG-ASN : angle 3.24734 / 1.99 ( 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 : 0.408 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: 0.7084 (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: 0.0883 time to fit residues: 27.7904 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 : 0.298 ------------------------------------------------------------------------------- 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... 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 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3940 r_free = 0.3940 target = 0.145679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.104058 restraints weight = 16283.032| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.50 r_work: 0.3241 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10503 Z= 0.221 Angle : 0.666 9.077 14252 Z= 0.327 Chirality : 0.047 0.225 1559 Planarity : 0.005 0.063 1822 Dihedral : 15.607 114.614 1570 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.83 % Allowed : 12.37 % Favored : 83.81 % 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: 2.02 (0.29), residues: 323 sheet: -0.76 (0.35), residues: 239 loop : -0.71 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 490 TYR 0.014 0.001 TYR D 50 PHE 0.018 0.002 PHE A 781 TRP 0.015 0.001 TRP B 312 HIS 0.003 0.001 HIS A 663 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.22 (10467) covalent geometry : angle 0.64919 / 0.32 (14178) SS BOND : bond 0.00398 / 0.24 ( 25) SS BOND : angle 0.98817 / 0.82 ( 50) hydrogen bonds : bond 0.04797 / 3.33 ( 374) hydrogen bonds : angle 5.94095 / 4.38 ( 1035) metal coordination : bond 0.01235 / 0.62 ( 3) link_BETA1-4 : bond 0.01932 / 1.02 ( 1) link_BETA1-4 : angle 2.45410 / 1.46 ( 3) link_NAG-ASN : bond 0.00475 / 0.27 ( 7) link_NAG-ASN : angle 3.62386 / 2.45 ( 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 163 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 120 time to evaluate : 0.318 Fit side-chains REVERT: A 459 PHE cc_start: 0.6861 (t80) cc_final: 0.6194 (t80) REVERT: A 572 LYS cc_start: 0.9098 (tptp) cc_final: 0.8832 (mtmt) REVERT: A 635 MET cc_start: 0.8157 (mmm) cc_final: 0.7271 (mmt) REVERT: A 746 ARG cc_start: 0.5436 (tpp80) cc_final: 0.4429 (ptt-90) REVERT: D 107 ASP cc_start: 0.8683 (m-30) cc_final: 0.8481 (m-30) REVERT: B 319 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7833 (tm-30) REVERT: B 449 MET cc_start: 0.8483 (mmt) cc_final: 0.8010 (mtt) REVERT: B 642 GLU cc_start: 0.7275 (tp30) cc_final: 0.6784 (pp20) outliers start: 43 outliers final: 28 residues processed: 148 average time/residue: 0.0752 time to fit residues: 16.4069 Evaluate side-chains 134 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 78 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 66 optimal weight: 0.0470 chunk 8 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 53 optimal weight: 0.0470 chunk 60 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 31 optimal weight: 0.0670 overall best weight: 0.4314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3969 r_free = 0.3969 target = 0.147999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.106960 restraints weight = 16441.640| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.57 r_work: 0.3293 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10503 Z= 0.122 Angle : 0.606 9.583 14252 Z= 0.289 Chirality : 0.044 0.206 1559 Planarity : 0.004 0.060 1822 Dihedral : 14.428 114.105 1567 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.20 % Allowed : 14.41 % 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: 0.10 (0.24), residues: 1269 helix: 2.14 (0.29), residues: 324 sheet: -0.63 (0.34), residues: 236 loop : -0.65 (0.24), residues: 709 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 0.018 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/Z covalent geometry : bond 0.00261 / 0.12 (10467) covalent geometry : angle 0.58862 / 0.29 (14178) SS BOND : bond 0.00185 / 0.11 ( 25) SS BOND : angle 0.65120 / 0.53 ( 50) hydrogen bonds : bond 0.03977 / 2.75 ( 374) hydrogen bonds : angle 5.37928 / 3.97 ( 1035) metal coordination : bond 0.00279 / 0.14 ( 3) link_BETA1-4 : bond 0.01660 / 0.87 ( 1) link_BETA1-4 : angle 2.48896 / 1.72 ( 3) link_NAG-ASN : bond 0.01021 / 0.57 ( 7) link_NAG-ASN : angle 3.70538 / 2.88 ( 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 162 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 459 PHE cc_start: 0.6816 (t80) cc_final: 0.6166 (t80) REVERT: A 572 LYS cc_start: 0.9171 (tptp) cc_final: 0.8855 (mtmt) REVERT: A 635 MET cc_start: 0.8146 (mmm) cc_final: 0.7470 (mmt) REVERT: A 746 ARG cc_start: 0.5427 (tpp80) cc_final: 0.4442 (ptt-90) REVERT: C 42 LYS cc_start: 0.7565 (mmmt) cc_final: 0.6810 (mtpt) REVERT: B 319 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7833 (tm-30) REVERT: B 449 MET cc_start: 0.8482 (mmt) cc_final: 0.7958 (mtt) REVERT: B 490 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.6818 (t0) REVERT: B 642 GLU cc_start: 0.7272 (tp30) cc_final: 0.6759 (pp20) outliers start: 36 outliers final: 23 residues processed: 151 average time/residue: 0.0682 time to fit residues: 15.2645 Evaluate side-chains 133 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 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 119 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 156 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 81 optimal weight: 0.9980 chunk 25 optimal weight: 0.0980 chunk 78 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 91 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3963 r_free = 0.3963 target = 0.147574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.106660 restraints weight = 16546.823| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 3.57 r_work: 0.3291 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10503 Z= 0.126 Angle : 0.586 9.241 14252 Z= 0.281 Chirality : 0.044 0.214 1559 Planarity : 0.004 0.061 1822 Dihedral : 13.107 112.095 1564 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.00 % Allowed : 14.95 % Favored : 81.05 % 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: 0.17 (0.24), residues: 1269 helix: 2.19 (0.29), residues: 323 sheet: -0.54 (0.35), residues: 236 loop : -0.63 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 490 TYR 0.010 0.001 TYR B 369 PHE 0.012 0.001 PHE B 527 TRP 0.012 0.001 TRP B 312 HIS 0.002 0.000 HIS A 663 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (10467) covalent geometry : angle 0.57314 / 0.28 (14178) SS BOND : bond 0.00216 / 0.13 ( 25) SS BOND : angle 0.69891 / 0.56 ( 50) hydrogen bonds : bond 0.03664 / 2.56 ( 374) hydrogen bonds : angle 5.08118 / 3.76 ( 1035) metal coordination : bond 0.00365 / 0.19 ( 3) link_BETA1-4 : bond 0.01678 / 0.88 ( 1) link_BETA1-4 : angle 2.71379 / 2.03 ( 3) link_NAG-ASN : bond 0.00606 / 0.36 ( 7) link_NAG-ASN : angle 2.95441 / 2.00 ( 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 161 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 116 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 459 PHE cc_start: 0.6842 (t80) cc_final: 0.6158 (t80) REVERT: A 572 LYS cc_start: 0.9213 (tptp) cc_final: 0.8878 (mtmt) REVERT: A 714 ARG cc_start: 0.7526 (tpp-160) cc_final: 0.6992 (tpp80) REVERT: A 746 ARG cc_start: 0.5477 (tpp80) cc_final: 0.4470 (ptt-90) REVERT: C 42 LYS cc_start: 0.7507 (mmmt) cc_final: 0.6715 (mtpt) REVERT: B 319 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7872 (tm-30) REVERT: B 449 MET cc_start: 0.8490 (mmt) cc_final: 0.7953 (mtt) REVERT: B 484 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.6975 (m-30) REVERT: B 642 GLU cc_start: 0.7272 (tp30) cc_final: 0.6803 (pp20) outliers start: 45 outliers final: 29 residues processed: 148 average time/residue: 0.0721 time to fit residues: 15.9145 Evaluate side-chains 136 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 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 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 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 348 LEU Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 484 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 34 optimal weight: 0.2980 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3967 r_free = 0.3967 target = 0.147903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.107088 restraints weight = 16434.927| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.54 r_work: 0.3296 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2446 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= 0.120 Angle : 0.590 9.662 14252 Z= 0.278 Chirality : 0.044 0.215 1559 Planarity : 0.004 0.063 1822 Dihedral : 12.772 110.929 1564 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.65 % Allowed : 16.19 % 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: 0.21 (0.24), residues: 1269 helix: 2.20 (0.29), residues: 324 sheet: -0.55 (0.35), residues: 237 loop : -0.58 (0.24), residues: 708 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 0.020 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/Z covalent geometry : bond 0.00271 / 0.12 (10467) covalent geometry : angle 0.57823 / 0.28 (14178) SS BOND : bond 0.00205 / 0.13 ( 25) SS BOND : angle 0.64359 / 0.52 ( 50) hydrogen bonds : bond 0.03441 / 2.40 ( 374) hydrogen bonds : angle 4.91492 / 3.66 ( 1035) metal coordination : bond 0.00292 / 0.15 ( 3) link_BETA1-4 : bond 0.01483 / 0.78 ( 1) link_BETA1-4 : angle 3.16223 / 2.42 ( 3) link_NAG-ASN : bond 0.00554 / 0.34 ( 7) link_NAG-ASN : angle 2.91503 / 1.96 ( 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: 41 poor density : 115 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 572 LYS cc_start: 0.9234 (tptp) cc_final: 0.8866 (mtmt) REVERT: A 714 ARG cc_start: 0.7523 (tpp-160) cc_final: 0.6978 (tpp80) REVERT: A 746 ARG cc_start: 0.5508 (tpp80) cc_final: 0.4466 (ptt-90) REVERT: C 4 MET cc_start: 0.8483 (mtp) cc_final: 0.7588 (mtp) REVERT: C 42 LYS cc_start: 0.7486 (mmmt) cc_final: 0.6682 (mtpt) REVERT: D 80 TYR cc_start: 0.8872 (m-80) cc_final: 0.8643 (m-80) REVERT: B 319 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7866 (tm-30) REVERT: B 449 MET cc_start: 0.8471 (mmt) cc_final: 0.7928 (mtt) REVERT: B 484 ASP cc_start: 0.7321 (OUTLIER) cc_final: 0.6899 (m-30) REVERT: B 642 GLU cc_start: 0.7347 (tp30) cc_final: 0.6848 (pp20) outliers start: 41 outliers final: 30 residues processed: 145 average time/residue: 0.0739 time to fit residues: 16.2088 Evaluate side-chains 133 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 732 VAL 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 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 484 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 50 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 110 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 69 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3970 r_free = 0.3970 target = 0.148261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.107397 restraints weight = 16567.389| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.57 r_work: 0.3299 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10503 Z= 0.118 Angle : 0.588 9.254 14252 Z= 0.278 Chirality : 0.044 0.186 1559 Planarity : 0.004 0.067 1822 Dihedral : 12.220 109.570 1564 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.38 % Allowed : 16.28 % Favored : 80.34 % 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: 0.27 (0.24), residues: 1269 helix: 2.24 (0.29), residues: 326 sheet: -0.60 (0.34), residues: 247 loop : -0.50 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 24 TYR 0.010 0.001 TYR B 369 PHE 0.021 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/Z covalent geometry : bond 0.00265 / 0.12 (10467) covalent geometry : angle 0.57463 / 0.28 (14178) SS BOND : bond 0.00194 / 0.14 ( 25) SS BOND : angle 0.71808 / 0.57 ( 50) hydrogen bonds : bond 0.03370 / 2.34 ( 374) hydrogen bonds : angle 4.80707 / 3.58 ( 1035) metal coordination : bond 0.00215 / 0.11 ( 3) link_BETA1-4 : bond 0.01404 / 0.74 ( 1) link_BETA1-4 : angle 3.56247 / 2.71 ( 3) link_NAG-ASN : bond 0.00527 / 0.33 ( 7) link_NAG-ASN : angle 2.90824 / 1.98 ( 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 147 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 572 LYS cc_start: 0.9303 (tptp) cc_final: 0.8906 (mtmt) REVERT: A 714 ARG cc_start: 0.7543 (tpp-160) cc_final: 0.6993 (tpp80) REVERT: A 727 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7746 (tt) REVERT: A 746 ARG cc_start: 0.5563 (tpp80) cc_final: 0.4479 (ptt180) REVERT: C 4 MET cc_start: 0.8533 (mtp) cc_final: 0.7656 (mtp) REVERT: C 42 LYS cc_start: 0.7447 (mmmt) cc_final: 0.6634 (mtpt) REVERT: D 73 ASP cc_start: 0.8539 (t0) cc_final: 0.7976 (t0) REVERT: B 319 GLU cc_start: 0.8422 (tm-30) cc_final: 0.7893 (tm-30) REVERT: B 449 MET cc_start: 0.8450 (mmt) cc_final: 0.7911 (mtt) REVERT: B 484 ASP cc_start: 0.7244 (OUTLIER) cc_final: 0.6814 (m-30) REVERT: B 642 GLU cc_start: 0.7422 (tp30) cc_final: 0.6910 (pp20) outliers start: 38 outliers final: 30 residues processed: 135 average time/residue: 0.0715 time to fit residues: 14.3554 Evaluate side-chains 133 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 654 TYR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 727 LEU 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 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 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 484 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 676 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 9 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 117 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.147117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.106361 restraints weight = 16463.208| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 3.54 r_work: 0.3283 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2692 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= 0.137 Angle : 0.593 9.496 14252 Z= 0.282 Chirality : 0.044 0.184 1559 Planarity : 0.004 0.065 1822 Dihedral : 11.864 108.359 1562 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.20 % Allowed : 16.73 % 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: 0.32 (0.25), residues: 1269 helix: 2.31 (0.29), residues: 326 sheet: -0.56 (0.34), residues: 246 loop : -0.49 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 24 TYR 0.012 0.001 TYR D 80 PHE 0.021 0.001 PHE B 581 TRP 0.010 0.001 TRP B 312 HIS 0.003 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (10467) covalent geometry : angle 0.57902 / 0.28 (14178) SS BOND : bond 0.00219 / 0.14 ( 25) SS BOND : angle 0.78970 / 0.64 ( 50) hydrogen bonds : bond 0.03381 / 2.36 ( 374) hydrogen bonds : angle 4.79330 / 3.57 ( 1035) metal coordination : bond 0.00287 / 0.15 ( 3) link_BETA1-4 : bond 0.01187 / 0.62 ( 1) link_BETA1-4 : angle 3.72891 / 2.77 ( 3) link_NAG-ASN : bond 0.00494 / 0.31 ( 7) link_NAG-ASN : angle 2.98217 / 2.05 ( 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 145 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 459 PHE cc_start: 0.6861 (t80) cc_final: 0.6167 (t80) REVERT: A 572 LYS cc_start: 0.9278 (tptp) cc_final: 0.8897 (mtmt) REVERT: A 714 ARG cc_start: 0.7574 (tpp-160) cc_final: 0.6988 (tpp80) REVERT: A 746 ARG cc_start: 0.5583 (tpp80) cc_final: 0.4501 (ptt-90) REVERT: A 786 PHE cc_start: 0.6788 (m-80) cc_final: 0.6444 (m-80) REVERT: C 4 MET cc_start: 0.8546 (mtp) cc_final: 0.7684 (mtp) REVERT: C 42 LYS cc_start: 0.7535 (mmmt) cc_final: 0.6726 (mtpt) REVERT: D 73 ASP cc_start: 0.8591 (t0) cc_final: 0.8351 (t0) REVERT: D 80 TYR cc_start: 0.8813 (m-80) cc_final: 0.8604 (m-80) REVERT: D 95 TYR cc_start: 0.8896 (m-80) cc_final: 0.8514 (m-80) REVERT: B 319 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7882 (tm-30) REVERT: B 449 MET cc_start: 0.8436 (mmt) cc_final: 0.7909 (mtt) REVERT: B 484 ASP cc_start: 0.7221 (OUTLIER) cc_final: 0.6806 (m-30) REVERT: B 642 GLU cc_start: 0.7415 (tp30) cc_final: 0.6872 (tm-30) REVERT: B 646 GLN cc_start: 0.6938 (tp-100) cc_final: 0.6513 (tp-100) outliers start: 36 outliers final: 33 residues processed: 135 average time/residue: 0.0746 time to fit residues: 14.8790 Evaluate side-chains 136 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 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 224 THR 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 484 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 59 optimal weight: 0.2980 chunk 82 optimal weight: 0.0770 chunk 123 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 90 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3986 r_free = 0.3986 target = 0.149783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.109133 restraints weight = 16430.202| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 3.54 r_work: 0.3313 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10503 Z= 0.104 Angle : 0.587 15.112 14252 Z= 0.274 Chirality : 0.043 0.194 1559 Planarity : 0.004 0.066 1822 Dihedral : 11.385 107.220 1562 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.02 % Allowed : 16.73 % 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: 0.40 (0.24), residues: 1269 helix: 2.35 (0.28), residues: 327 sheet: -0.47 (0.35), residues: 236 loop : -0.44 (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 0.023 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/Z covalent geometry : bond 0.00229 / 0.10 (10467) covalent geometry : angle 0.57309 / 0.27 (14178) SS BOND : bond 0.00185 / 0.11 ( 25) SS BOND : angle 0.65185 / 0.53 ( 50) hydrogen bonds : bond 0.03178 / 2.21 ( 374) hydrogen bonds : angle 4.68592 / 3.49 ( 1035) metal coordination : bond 0.00107 / 0.05 ( 3) link_BETA1-4 : bond 0.00982 / 0.52 ( 1) link_BETA1-4 : angle 3.58777 / 2.56 ( 3) link_NAG-ASN : bond 0.00521 / 0.33 ( 7) link_NAG-ASN : angle 3.01488 / 2.03 ( 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 146 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 459 PHE cc_start: 0.6862 (t80) cc_final: 0.6181 (t80) REVERT: A 572 LYS cc_start: 0.9323 (tptp) cc_final: 0.8937 (mtmt) REVERT: A 746 ARG cc_start: 0.5587 (tpp80) cc_final: 0.4491 (ptt-90) REVERT: A 786 PHE cc_start: 0.6631 (m-80) cc_final: 0.6350 (m-80) REVERT: C 4 MET cc_start: 0.8548 (mtp) cc_final: 0.7652 (mtp) REVERT: C 42 LYS cc_start: 0.7408 (mmmt) cc_final: 0.6593 (mtpt) REVERT: D 73 ASP cc_start: 0.8595 (t0) cc_final: 0.8086 (t0) REVERT: D 80 TYR cc_start: 0.8822 (m-80) cc_final: 0.8587 (m-80) REVERT: B 319 GLU cc_start: 0.8448 (tm-30) cc_final: 0.7941 (tm-30) REVERT: B 449 MET cc_start: 0.8405 (mmt) cc_final: 0.7886 (mtt) REVERT: B 484 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6804 (m-30) REVERT: B 642 GLU cc_start: 0.7459 (tp30) cc_final: 0.6929 (tm-30) outliers start: 34 outliers final: 27 residues processed: 136 average time/residue: 0.0731 time to fit residues: 14.6213 Evaluate side-chains 132 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 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 224 THR 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 484 ASP Chi-restraints excluded: chain B residue 538 ILE 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: 0.5980 chunk 37 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 92 optimal weight: 0.2980 chunk 38 optimal weight: 0.3980 chunk 35 optimal weight: 6.9990 chunk 18 optimal weight: 0.0980 chunk 46 optimal weight: 0.9980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3974 r_free = 0.3974 target = 0.148553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.108437 restraints weight = 16371.011| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.53 r_work: 0.3316 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10503 Z= 0.105 Angle : 0.586 13.769 14252 Z= 0.273 Chirality : 0.043 0.191 1559 Planarity : 0.004 0.068 1822 Dihedral : 11.066 106.778 1562 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.85 % Allowed : 16.90 % 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: 0.45 (0.24), residues: 1269 helix: 2.43 (0.29), residues: 326 sheet: -0.43 (0.35), residues: 236 loop : -0.44 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 24 TYR 0.011 0.001 TYR D 95 PHE 0.023 0.001 PHE B 581 TRP 0.010 0.001 TRP B 312 HIS 0.002 0.000 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (10467) covalent geometry : angle 0.57133 / 0.27 (14178) SS BOND : bond 0.00150 / 0.09 ( 25) SS BOND : angle 0.63751 / 0.51 ( 50) hydrogen bonds : bond 0.03106 / 2.16 ( 374) hydrogen bonds : angle 4.61575 / 3.43 ( 1035) metal coordination : bond 0.00142 / 0.07 ( 3) link_BETA1-4 : bond 0.00842 / 0.44 ( 1) link_BETA1-4 : angle 3.51906 / 2.44 ( 3) link_NAG-ASN : bond 0.00502 / 0.32 ( 7) link_NAG-ASN : angle 3.09803 / 2.10 ( 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 139 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 572 LYS cc_start: 0.9305 (tptp) cc_final: 0.8973 (tptp) REVERT: A 678 THR cc_start: 0.7725 (t) cc_final: 0.7517 (t) REVERT: A 746 ARG cc_start: 0.5496 (tpp80) cc_final: 0.4412 (ptt-90) REVERT: A 786 PHE cc_start: 0.6539 (m-80) cc_final: 0.6290 (m-80) REVERT: C 4 MET cc_start: 0.8541 (mtp) cc_final: 0.7647 (mtp) REVERT: D 73 ASP cc_start: 0.8558 (t0) cc_final: 0.8037 (t0) REVERT: D 80 TYR cc_start: 0.8769 (m-80) cc_final: 0.8510 (m-80) REVERT: B 319 GLU cc_start: 0.8406 (tm-30) cc_final: 0.7883 (tm-30) REVERT: B 449 MET cc_start: 0.8349 (mmt) cc_final: 0.7821 (mtt) REVERT: B 484 ASP cc_start: 0.7129 (OUTLIER) cc_final: 0.6736 (m-30) REVERT: B 490 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7006 (t0) REVERT: B 642 GLU cc_start: 0.7453 (tp30) cc_final: 0.6905 (tm-30) outliers start: 32 outliers final: 26 residues processed: 131 average time/residue: 0.0734 time to fit residues: 14.4176 Evaluate side-chains 132 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 GLN 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 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 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 247 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 538 ILE 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: 8.9990 chunk 79 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.0070 chunk 24 optimal weight: 0.8980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3959 r_free = 0.3959 target = 0.147361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.106988 restraints weight = 16298.974| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 3.53 r_work: 0.3300 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2985 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= 0.117 Angle : 0.599 14.488 14252 Z= 0.279 Chirality : 0.043 0.193 1559 Planarity : 0.004 0.071 1822 Dihedral : 10.772 106.203 1562 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.76 % Allowed : 17.17 % 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: 0.46 (0.25), residues: 1269 helix: 2.45 (0.29), residues: 326 sheet: -0.45 (0.34), residues: 246 loop : -0.42 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 24 TYR 0.011 0.001 TYR D 95 PHE 0.022 0.001 PHE B 581 TRP 0.009 0.001 TRP B 312 HIS 0.002 0.000 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (10467) covalent geometry : angle 0.58354 / 0.28 (14178) SS BOND : bond 0.00172 / 0.12 ( 25) SS BOND : angle 0.70909 / 0.57 ( 50) hydrogen bonds : bond 0.03147 / 2.20 ( 374) hydrogen bonds : angle 4.59196 / 3.43 ( 1035) metal coordination : bond 0.00200 / 0.10 ( 3) link_BETA1-4 : bond 0.00781 / 0.41 ( 1) link_BETA1-4 : angle 3.43299 / 2.27 ( 3) link_NAG-ASN : bond 0.00477 / 0.30 ( 7) link_NAG-ASN : angle 3.23103 / 2.20 ( 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 142 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 572 LYS cc_start: 0.9372 (tptp) cc_final: 0.8943 (mtmt) REVERT: A 678 THR cc_start: 0.7775 (t) cc_final: 0.7550 (t) REVERT: A 746 ARG cc_start: 0.5480 (tpp80) cc_final: 0.4398 (ptt-90) REVERT: A 786 PHE cc_start: 0.6566 (m-80) cc_final: 0.6317 (m-80) REVERT: C 4 MET cc_start: 0.8536 (mtp) cc_final: 0.7631 (mtp) REVERT: C 42 LYS cc_start: 0.7317 (mmmt) cc_final: 0.6598 (mtpt) REVERT: D 73 ASP cc_start: 0.8621 (t0) cc_final: 0.8118 (t0) REVERT: B 319 GLU cc_start: 0.8419 (tm-30) cc_final: 0.7705 (tm-30) REVERT: B 449 MET cc_start: 0.8367 (mmt) cc_final: 0.7873 (mtt) REVERT: B 484 ASP cc_start: 0.7131 (OUTLIER) cc_final: 0.6739 (m-30) REVERT: B 490 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7082 (t0) REVERT: B 642 GLU cc_start: 0.7451 (tp30) cc_final: 0.6881 (tm-30) outliers start: 31 outliers final: 28 residues processed: 135 average time/residue: 0.0765 time to fit residues: 15.4142 Evaluate side-chains 137 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 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 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 247 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 538 ILE 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 62 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 58 optimal weight: 0.0570 chunk 123 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3958 r_free = 0.3958 target = 0.147307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.106366 restraints weight = 16627.875| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.58 r_work: 0.3281 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3009 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= 0.134 Angle : 0.607 14.470 14252 Z= 0.284 Chirality : 0.043 0.194 1559 Planarity : 0.004 0.071 1822 Dihedral : 10.557 105.741 1562 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.94 % Allowed : 16.90 % 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: 0.47 (0.25), residues: 1269 helix: 2.46 (0.29), residues: 326 sheet: -0.44 (0.34), residues: 246 loop : -0.42 (0.25), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 24 TYR 0.010 0.001 TYR D 50 PHE 0.023 0.001 PHE B 581 TRP 0.010 0.001 TRP A 745 HIS 0.003 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (10467) covalent geometry : angle 0.59018 / 0.28 (14178) SS BOND : bond 0.00226 / 0.14 ( 25) SS BOND : angle 0.78636 / 0.63 ( 50) hydrogen bonds : bond 0.03228 / 2.26 ( 374) hydrogen bonds : angle 4.62931 / 3.45 ( 1035) metal coordination : bond 0.00253 / 0.13 ( 3) link_BETA1-4 : bond 0.00687 / 0.36 ( 1) link_BETA1-4 : angle 3.26669 / 2.04 ( 3) link_NAG-ASN : bond 0.00469 / 0.29 ( 7) link_NAG-ASN : angle 3.39557 / 2.32 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2335.29 seconds wall clock time: 40 minutes 38.51 seconds (2438.51 seconds total)