Starting phenix.real_space_refine on Wed Jul 30 12:37:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gce_29932/07_2025/8gce_29932.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gce_29932/07_2025/8gce_29932.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/8gce_29932/07_2025/8gce_29932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gce_29932/07_2025/8gce_29932.map" model { file = "/net/cci-nas-00/data/ceres_data/8gce_29932/07_2025/8gce_29932.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gce_29932/07_2025/8gce_29932.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.001 sd= 0.049 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 6 9.91 5 Mg 1 5.21 5 S 98 5.16 5 C 7697 2.51 5 N 2116 2.21 5 O 2425 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12343 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7007 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 912, 6966 Classifications: {'peptide': 912} Link IDs: {'PCIS': 2, 'PTRANS': 59, 'TRANS': 850} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 912, 6966 Classifications: {'peptide': 912} Link IDs: {'PCIS': 2, 'PTRANS': 59, 'TRANS': 850} Chain breaks: 2 bond proxies already assigned to first conformer: 7082 Chain: "B" Number of atoms: 5195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 676, 5191 Classifications: {'peptide': 676} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 643} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 676, 5191 Classifications: {'peptide': 676} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 643} Chain breaks: 2 bond proxies already assigned to first conformer: 5277 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 32 Unusual residues: {' CA': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 72 residue: pdb=" N AGLN A 177 " occ=0.51 ... (16 atoms not shown) pdb=" NE2BGLN A 177 " occ=0.49 residue: pdb=" N AARG A 276 " occ=0.92 ... (20 atoms not shown) pdb=" NH2BARG A 276 " occ=0.08 residue: pdb=" N AHIS A 587 " occ=0.40 ... (18 atoms not shown) pdb=" NE2BHIS A 587 " occ=0.60 residue: pdb=" N PRO B 605 " occ=0.71 ... (5 atoms not shown) pdb=" CD PRO B 605 " occ=0.71 residue: pdb=" N ASP B 606 " occ=0.49 ... (6 atoms not shown) pdb=" OD2 ASP B 606 " occ=0.49 residue: pdb=" N ALA B 607 " occ=0.70 ... (3 atoms not shown) pdb=" CB ALA B 607 " occ=0.70 residue: pdb=" N CYS B 608 " occ=0.50 ... (4 atoms not shown) pdb=" SG CYS B 608 " occ=0.50 residue: pdb=" N THR B 609 " occ=0.56 ... (5 atoms not shown) pdb=" CG2 THR B 609 " occ=0.56 residue: pdb=" N PHE B 610 " occ=0.93 ... (9 atoms not shown) pdb=" CZ PHE B 610 " occ=0.93 residue: pdb=" N LYS B 611 " occ=0.77 ... (7 atoms not shown) pdb=" NZ LYS B 611 " occ=0.77 residue: pdb=" N LYS B 612 " occ=0.67 ... (7 atoms not shown) pdb=" NZ LYS B 612 " occ=0.67 residue: pdb=" N GLU B 613 " occ=0.76 ... (7 atoms not shown) pdb=" OE2 GLU B 613 " occ=0.76 ... (remaining 60 not shown) Time building chain proxies: 13.22, per 1000 atoms: 1.07 Number of scatterers: 12343 At special positions: 0 Unit cell: (104.86, 123.05, 129.47, 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) Ca 6 19.99 S 98 16.00 Mg 1 11.99 O 2425 8.00 N 2116 7.00 C 7697 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 167 " distance=2.02 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 545 " distance=2.03 Simple disulfide: pdb=" SG CYS A 602 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 674 " - pdb=" SG CYS A 687 " distance=2.04 Simple disulfide: pdb=" SG CYS A 826 " - pdb=" SG CYS A 890 " distance=2.03 Simple disulfide: pdb=" SG CYS A 880 " - pdb=" SG CYS A 885 " distance=2.03 Simple disulfide: pdb=" SG CYS B 5 " - pdb=" SG CYS B 23 " distance=2.03 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 435 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 38 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 386 " distance=2.04 Simple disulfide: pdb=" SG CYS B 406 " - pdb=" SG CYS B 433 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 448 " - pdb=" SG CYS B 460 " distance=2.03 Simple disulfide: pdb=" SG CYS B 462 " - pdb=" SG CYS B 471 " distance=2.03 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 503 " distance=2.03 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 501 " distance=2.03 Simple disulfide: pdb=" SG CYS B 495 " - pdb=" SG CYS B 506 " distance=2.03 Simple disulfide: pdb=" SG CYS B 508 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 523 " - pdb=" SG CYS B 544 " distance=2.03 Simple disulfide: pdb=" SG CYS B 528 " - pdb=" SG CYS B 542 " distance=2.04 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 547 " distance=2.03 Simple disulfide: pdb=" SG CYS B 549 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 560 " - pdb=" SG CYS B 583 " distance=2.03 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 581 " distance=2.02 Simple disulfide: pdb=" SG CYS B 575 " - pdb=" SG CYS B 586 " distance=2.03 Simple disulfide: pdb=" SG CYS B 588 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 655 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 631 " 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 C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1105 " - " ASN A 15 " " NAG A1106 " - " ASN A 570 " " NAG C 1 " - " ASN B 371 " " NAG D 1 " - " ASN B 320 " " NAG E 1 " - " ASN B 99 " Time building additional restraints: 3.20 Conformation dependent library (CDL) restraints added in 3.3 seconds 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2920 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 25 sheets defined 10.2% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.545A pdb=" N ILE A 203 " --> pdb=" O PRO A 199 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A 204 " --> pdb=" O VAL A 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 199 through 204' Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.567A pdb=" N GLN A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 9 removed outlier: 3.557A pdb=" N ARG B 8 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY B 9 " --> pdb=" O CYS B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 20 removed outlier: 4.195A pdb=" N SER B 20 " --> pdb=" O CYS B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 Processing helix chain 'B' and resid 50 through 52 No H-bonds generated for 'chain 'B' and resid 50 through 52' Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 124 through 132 Processing helix chain 'B' and resid 135 through 143 removed outlier: 3.943A pdb=" N GLN B 141 " --> pdb=" O LYS B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.636A pdb=" N LEU B 173 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.948A pdb=" N ASN B 204 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 208 " --> pdb=" O ASN B 204 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 232 removed outlier: 4.309A pdb=" N ALA B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 258 through 264 removed outlier: 3.642A pdb=" N ARG B 261 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU B 262 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 286 removed outlier: 4.383A pdb=" N THR B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 314 through 319 Processing helix chain 'B' and resid 339 through 354 Processing helix chain 'B' and resid 493 through 497 Processing helix chain 'B' and resid 534 through 538 Processing helix chain 'B' and resid 612 through 617 Processing helix chain 'B' and resid 630 through 635 removed outlier: 4.039A pdb=" N TYR B 634 " --> pdb=" O THR B 630 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N CYS B 635 " --> pdb=" O CYS B 631 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 630 through 635' Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 10 removed outlier: 3.865A pdb=" N THR A 9 " --> pdb=" O VAL A 447 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 removed outlier: 3.612A pdb=" N HIS A 26 " --> pdb=" O ALA A 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 removed outlier: 4.900A pdb=" N VAL A 53 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.399A pdb=" N GLU A 75 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 256 through 257 removed outlier: 6.522A pdb=" N VAL A 267 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG A 279 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 269 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 293 through 296 removed outlier: 3.810A pdb=" N LEU A 345 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 314 through 315 Processing sheet with id=AA9, first strand: chain 'A' and resid 360 through 364 removed outlier: 5.866A pdb=" N ASP A 373 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 405 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 521 through 523 removed outlier: 3.672A pdb=" N LEU A 522 " --> pdb=" O PHE A 551 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 551 " --> pdb=" O LEU A 522 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 544 " --> pdb=" O VAL A 491 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 491 " --> pdb=" O ILE A 544 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR A 494 " --> pdb=" O LYS A 455 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL A 454 " --> pdb=" O VAL A 585 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N AHIS A 587 " --> pdb=" O VAL A 454 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.678A pdb=" N CYS A 473 " --> pdb=" O VAL A 482 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL A 482 " --> pdb=" O CYS A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 530 through 536 removed outlier: 4.143A pdb=" N ASN A 505 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER A 572 " --> pdb=" O ASN A 505 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU A 507 " --> pdb=" O ASN A 570 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASN A 570 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLN A 509 " --> pdb=" O SER A 568 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N SER A 568 " --> pdb=" O GLN A 509 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 612 through 615 removed outlier: 3.683A pdb=" N MET A 703 " --> pdb=" O LEU A 633 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 706 " --> pdb=" O HIS A 658 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 648 through 652 removed outlier: 4.232A pdb=" N GLN A 720 " --> pdb=" O HIS A 652 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 749 through 755 removed outlier: 3.581A pdb=" N GLU A 749 " --> pdb=" O HIS A 787 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N HIS A 787 " --> pdb=" O GLU A 749 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A 751 " --> pdb=" O GLU A 785 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 907 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS A 782 " --> pdb=" O VAL A 905 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 905 " --> pdb=" O HIS A 782 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR A 784 " --> pdb=" O VAL A 903 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 903 " --> pdb=" O TYR A 784 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N MET A 902 " --> pdb=" O PRO A 820 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR A 904 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ILE A 818 " --> pdb=" O THR A 904 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU A 906 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE A 908 " --> pdb=" O TYR A 814 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR A 814 " --> pdb=" O PHE A 908 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 825 through 829 removed outlier: 4.338A pdb=" N GLN A 825 " --> pdb=" O ASP A 891 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 887 " --> pdb=" O GLN A 829 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU A 894 " --> pdb=" O ASN A 795 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASN A 795 " --> pdb=" O GLU A 894 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N GLY A 796 " --> pdb=" O SER A 933 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 933 " --> pdb=" O GLY A 796 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N HIS A 802 " --> pdb=" O HIS A 927 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N HIS A 927 " --> pdb=" O HIS A 802 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 38 through 39 Processing sheet with id=AB9, first strand: chain 'B' and resid 60 through 65 removed outlier: 3.815A pdb=" N ARG B 62 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG B 87 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE B 88 " --> pdb=" O GLN B 428 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N THR B 430 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU B 90 " --> pdb=" O THR B 430 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 414 " --> pdb=" O VAL B 427 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 97 through 102 Processing sheet with id=AC2, first strand: chain 'B' and resid 194 through 197 removed outlier: 5.923A pdb=" N THR B 195 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N PHE B 153 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 151 " --> pdb=" O THR B 197 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 499 through 502 Processing sheet with id=AC4, first strand: chain 'B' and resid 540 through 543 Processing sheet with id=AC5, first strand: chain 'B' and resid 581 through 582 Processing sheet with id=AC6, first strand: chain 'B' and resid 638 through 639 removed outlier: 6.184A pdb=" N GLU B 638 " --> pdb=" O LEU B 679 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 655 through 658 removed outlier: 3.673A pdb=" N TYR B 657 " --> pdb=" O VAL B 665 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 665 " --> pdb=" O TYR B 657 " (cutoff:3.500A) 244 hydrogen bonds defined for protein. 632 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: 3.81 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2145 1.31 - 1.44: 3267 1.44 - 1.58: 7063 1.58 - 1.71: 1 1.71 - 1.85: 123 Bond restraints: 12599 Sorted by residual: bond pdb=" CA SER A 664 " pdb=" CB SER A 664 " ideal model delta sigma weight residual 1.530 1.363 0.167 1.69e-02 3.50e+03 9.75e+01 bond pdb=" CA LEU A 689 " pdb=" C LEU A 689 " ideal model delta sigma weight residual 1.523 1.422 0.101 1.34e-02 5.57e+03 5.66e+01 bond pdb=" CA ALA A 662 " pdb=" C ALA A 662 " ideal model delta sigma weight residual 1.523 1.429 0.094 1.34e-02 5.57e+03 4.90e+01 bond pdb=" CA ASN A 665 " pdb=" C ASN A 665 " ideal model delta sigma weight residual 1.524 1.427 0.096 1.59e-02 3.96e+03 3.67e+01 bond pdb=" CA ALA A 662 " pdb=" CB ALA A 662 " ideal model delta sigma weight residual 1.530 1.439 0.091 1.69e-02 3.50e+03 2.90e+01 ... (remaining 12594 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.77: 17022 5.77 - 11.54: 76 11.54 - 17.31: 16 17.31 - 23.08: 7 23.08 - 28.85: 1 Bond angle restraints: 17122 Sorted by residual: angle pdb=" N GLN A 18 " pdb=" CA GLN A 18 " pdb=" C GLN A 18 " ideal model delta sigma weight residual 110.41 92.07 18.34 1.18e+00 7.18e-01 2.42e+02 angle pdb=" C ASN A 691 " pdb=" N PRO A 692 " pdb=" CA PRO A 692 " ideal model delta sigma weight residual 119.84 101.42 18.42 1.25e+00 6.40e-01 2.17e+02 angle pdb=" C ARG A 661 " pdb=" CA ARG A 661 " pdb=" CB ARG A 661 " ideal model delta sigma weight residual 110.42 81.57 28.85 1.99e+00 2.53e-01 2.10e+02 angle pdb=" N ASN A 665 " pdb=" CA ASN A 665 " pdb=" C ASN A 665 " ideal model delta sigma weight residual 112.97 98.69 14.28 1.06e+00 8.90e-01 1.82e+02 angle pdb=" N LEU A 689 " pdb=" CA LEU A 689 " pdb=" CB LEU A 689 " ideal model delta sigma weight residual 110.49 88.84 21.65 1.69e+00 3.50e-01 1.64e+02 ... (remaining 17117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.51: 7211 24.51 - 49.02: 525 49.02 - 73.53: 72 73.53 - 98.04: 15 98.04 - 122.55: 9 Dihedral angle restraints: 7832 sinusoidal: 3269 harmonic: 4563 Sorted by residual: dihedral pdb=" CA ASN A 691 " pdb=" C ASN A 691 " pdb=" N PRO A 692 " pdb=" CA PRO A 692 " ideal model delta harmonic sigma weight residual -180.00 -57.45 -122.55 0 5.00e+00 4.00e-02 6.01e+02 dihedral pdb=" C ARG A 661 " pdb=" N ARG A 661 " pdb=" CA ARG A 661 " pdb=" CB ARG A 661 " ideal model delta harmonic sigma weight residual -122.60 -83.31 -39.29 0 2.50e+00 1.60e-01 2.47e+02 dihedral pdb=" N LEU A 689 " pdb=" C LEU A 689 " pdb=" CA LEU A 689 " pdb=" CB LEU A 689 " ideal model delta harmonic sigma weight residual 122.80 90.01 32.79 0 2.50e+00 1.60e-01 1.72e+02 ... (remaining 7829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.215: 1899 0.215 - 0.431: 16 0.431 - 0.646: 3 0.646 - 0.862: 1 0.862 - 1.077: 3 Chirality restraints: 1922 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.32 -1.08 2.00e-02 2.50e+03 2.90e+03 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.38e+02 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 -2.27 -0.13 2.00e-02 2.50e+03 4.37e+01 ... (remaining 1919 not shown) Planarity restraints: 2264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.365 2.00e-02 2.50e+03 3.08e-01 1.19e+03 pdb=" C7 NAG C 1 " 0.096 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.539 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " -0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " 0.333 2.00e-02 2.50e+03 2.89e-01 1.04e+03 pdb=" C7 NAG C 2 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " 0.079 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " -0.514 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " 0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.336 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG D 1 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.177 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.501 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.074 2.00e-02 2.50e+03 ... (remaining 2261 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.25: 25 2.25 - 2.91: 5679 2.91 - 3.57: 17632 3.57 - 4.24: 28454 4.24 - 4.90: 46088 Nonbonded interactions: 97878 Sorted by model distance: nonbonded pdb=" N LEU A 689 " pdb=" OD1 ASN A 691 " model vdw 1.584 3.120 nonbonded pdb=" CA LEU A 689 " pdb=" OD1 ASN A 691 " model vdw 1.759 3.470 nonbonded pdb=" C LEU A 689 " pdb=" OD1 ASN A 691 " model vdw 1.847 3.270 nonbonded pdb=" N ASN A 665 " pdb=" O GLY A 700 " model vdw 1.909 3.120 nonbonded pdb=" OE2 GLU B 220 " pdb="MG MG B2001 " model vdw 1.982 2.170 ... (remaining 97873 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } 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=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 38.220 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5559 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.167 12645 Z= 0.408 Angle : 1.166 28.849 17224 Z= 0.661 Chirality : 0.077 1.077 1922 Planarity : 0.015 0.308 2259 Dihedral : 16.738 122.547 4804 Min Nonbonded Distance : 1.584 Molprobity Statistics. All-atom Clashscore : 31.98 Ramachandran Plot: Outliers : 1.59 % Allowed : 9.58 % Favored : 88.83 % Rotamer: Outliers : 3.38 % Allowed : 17.57 % Favored : 79.04 % Cbeta Deviations : 1.03 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.20), residues: 1587 helix: -2.13 (0.43), residues: 122 sheet: -0.83 (0.26), residues: 425 loop : -1.84 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 113 HIS 0.007 0.001 HIS B 274 PHE 0.037 0.002 PHE A 669 TYR 0.029 0.002 TYR B 164 ARG 0.038 0.001 ARG A 661 Details of bonding type rmsd link_NAG-ASN : bond 0.01894 ( 5) link_NAG-ASN : angle 3.50567 ( 15) link_BETA1-4 : bond 0.00816 ( 5) link_BETA1-4 : angle 4.24233 ( 15) hydrogen bonds : bond 0.28179 ( 244) hydrogen bonds : angle 11.08730 ( 632) SS BOND : bond 0.00443 ( 36) SS BOND : angle 1.62065 ( 72) covalent geometry : bond 0.00693 (12599) covalent geometry : angle 1.15296 (17122) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLN cc_start: 0.7898 (mt0) cc_final: 0.7512 (tt0) REVERT: A 112 HIS cc_start: 0.4661 (m90) cc_final: 0.4455 (m170) REVERT: A 121 GLU cc_start: 0.2824 (mp0) cc_final: 0.2220 (tt0) REVERT: A 124 LYS cc_start: 0.2962 (mtmm) cc_final: 0.2582 (mtmm) REVERT: A 164 LYS cc_start: 0.5149 (pttt) cc_final: 0.4624 (pttm) REVERT: A 449 ARG cc_start: 0.5775 (mpp80) cc_final: 0.4968 (mtp180) REVERT: A 489 MET cc_start: 0.5934 (ppp) cc_final: 0.5655 (tpt) REVERT: A 660 MET cc_start: 0.4302 (mmm) cc_final: 0.3346 (mmt) REVERT: A 691 ASN cc_start: 0.7019 (OUTLIER) cc_final: 0.6490 (m110) REVERT: A 835 LEU cc_start: 0.1899 (OUTLIER) cc_final: 0.0928 (mt) REVERT: A 837 VAL cc_start: 0.1859 (OUTLIER) cc_final: 0.1241 (m) outliers start: 45 outliers final: 18 residues processed: 202 average time/residue: 0.2811 time to fit residues: 79.9676 Evaluate side-chains 115 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 PRO Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 670 GLU Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 507 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 47 optimal weight: 20.0000 chunk 75 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 143 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 ASN A 665 ASN A 808 GLN A 833 ASN B 79 GLN B 255 HIS B 319 GLN ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.228266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.200866 restraints weight = 35698.255| |-----------------------------------------------------------------------------| r_work (start): 0.4617 rms_B_bonded: 5.26 r_work (final): 0.4617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4614 r_free = 0.4614 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4611 r_free = 0.4611 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| r_final: 0.4611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5512 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.125 12645 Z= 0.300 Angle : 0.977 12.005 17224 Z= 0.491 Chirality : 0.055 0.472 1922 Planarity : 0.007 0.069 2259 Dihedral : 10.163 83.278 1968 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.58 % Favored : 90.16 % Rotamer: Outliers : 3.82 % Allowed : 17.43 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.20), residues: 1587 helix: -2.30 (0.42), residues: 117 sheet: -1.21 (0.25), residues: 441 loop : -1.98 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 553 HIS 0.010 0.001 HIS A 112 PHE 0.029 0.004 PHE B 153 TYR 0.027 0.003 TYR A 190 ARG 0.012 0.001 ARG A 661 Details of bonding type rmsd link_NAG-ASN : bond 0.01162 ( 5) link_NAG-ASN : angle 4.31579 ( 15) link_BETA1-4 : bond 0.01115 ( 5) link_BETA1-4 : angle 4.10631 ( 15) hydrogen bonds : bond 0.05738 ( 244) hydrogen bonds : angle 8.24106 ( 632) SS BOND : bond 0.00511 ( 36) SS BOND : angle 1.78533 ( 72) covalent geometry : bond 0.00690 (12599) covalent geometry : angle 0.95650 (17122) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 114 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ASN cc_start: 0.7020 (OUTLIER) cc_final: 0.6728 (m-40) REVERT: A 121 GLU cc_start: 0.2878 (mp0) cc_final: 0.2361 (tt0) REVERT: A 667 GLU cc_start: 0.4751 (OUTLIER) cc_final: 0.3361 (mm-30) REVERT: A 681 GLU cc_start: 0.3588 (OUTLIER) cc_final: 0.3333 (mt-10) REVERT: A 895 MET cc_start: -0.0843 (ttt) cc_final: -0.1330 (ttt) REVERT: A 902 MET cc_start: 0.6619 (pmm) cc_final: 0.5030 (tmm) REVERT: B 304 ILE cc_start: 0.5807 (mm) cc_final: 0.5594 (mm) REVERT: B 459 VAL cc_start: 0.4073 (OUTLIER) cc_final: 0.3740 (p) outliers start: 51 outliers final: 27 residues processed: 153 average time/residue: 0.2353 time to fit residues: 54.0926 Evaluate side-chains 124 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 681 GLU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 178 TYR Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 653 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 152 optimal weight: 20.0000 chunk 29 optimal weight: 0.5980 chunk 148 optimal weight: 0.9980 chunk 114 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 151 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN A 808 GLN ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4890 r_free = 0.4890 target = 0.231155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.193011 restraints weight = 45108.070| |-----------------------------------------------------------------------------| r_work (start): 0.4538 rms_B_bonded: 4.13 r_work: 0.4058 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4039 r_free = 0.4039 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4039 r_free = 0.4039 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| r_final: 0.4039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12645 Z= 0.174 Angle : 0.786 10.065 17224 Z= 0.391 Chirality : 0.049 0.302 1922 Planarity : 0.005 0.075 2259 Dihedral : 7.929 60.099 1943 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.26 % Favored : 90.42 % Rotamer: Outliers : 2.35 % Allowed : 19.26 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.20), residues: 1587 helix: -2.00 (0.42), residues: 122 sheet: -1.14 (0.24), residues: 453 loop : -1.82 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 238 HIS 0.004 0.001 HIS A 26 PHE 0.020 0.002 PHE A 669 TYR 0.019 0.002 TYR A 380 ARG 0.006 0.001 ARG B 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 5) link_NAG-ASN : angle 2.95792 ( 15) link_BETA1-4 : bond 0.01056 ( 5) link_BETA1-4 : angle 3.16389 ( 15) hydrogen bonds : bond 0.04231 ( 244) hydrogen bonds : angle 7.30019 ( 632) SS BOND : bond 0.00400 ( 36) SS BOND : angle 1.37674 ( 72) covalent geometry : bond 0.00394 (12599) covalent geometry : angle 0.77270 (17122) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 1.401 Fit side-chains revert: symmetry clash REVERT: A 84 LEU cc_start: 0.1116 (OUTLIER) cc_final: -0.0159 (mt) REVERT: A 164 LYS cc_start: 0.5948 (pttt) cc_final: 0.5581 (ptpp) REVERT: A 208 ARG cc_start: 0.6501 (OUTLIER) cc_final: 0.6161 (mmp80) REVERT: A 489 MET cc_start: 0.7696 (ppp) cc_final: 0.7367 (ppp) REVERT: A 520 ARG cc_start: 0.5935 (mmt180) cc_final: 0.5562 (mpt-90) REVERT: A 667 GLU cc_start: 0.4482 (OUTLIER) cc_final: 0.3210 (mm-30) REVERT: A 671 ARG cc_start: -0.0585 (OUTLIER) cc_final: -0.0946 (tmm-80) REVERT: A 681 GLU cc_start: 0.3345 (OUTLIER) cc_final: 0.2948 (mt-10) REVERT: A 902 MET cc_start: 0.6851 (pmm) cc_final: 0.4999 (tmm) REVERT: B 205 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6931 (mp0) REVERT: B 344 ILE cc_start: 0.5047 (OUTLIER) cc_final: 0.4346 (mt) REVERT: B 557 TYR cc_start: 0.5557 (t80) cc_final: 0.5061 (t80) outliers start: 31 outliers final: 14 residues processed: 132 average time/residue: 0.2272 time to fit residues: 45.5007 Evaluate side-chains 104 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 681 GLU Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 587 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 82 optimal weight: 0.4980 chunk 51 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 123 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 665 ASN ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4876 r_free = 0.4876 target = 0.229628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.195377 restraints weight = 53459.286| |-----------------------------------------------------------------------------| r_work (start): 0.4558 rms_B_bonded: 4.06 r_work: 0.4008 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3993 r_free = 0.3993 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3994 r_free = 0.3994 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| r_final: 0.3994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12645 Z= 0.210 Angle : 0.799 10.258 17224 Z= 0.399 Chirality : 0.050 0.477 1922 Planarity : 0.006 0.070 2259 Dihedral : 7.428 58.735 1943 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.71 % Favored : 89.97 % Rotamer: Outliers : 4.12 % Allowed : 18.31 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.20), residues: 1587 helix: -1.87 (0.44), residues: 121 sheet: -1.23 (0.24), residues: 448 loop : -1.84 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 553 HIS 0.005 0.001 HIS B 255 PHE 0.019 0.003 PHE A 669 TYR 0.022 0.002 TYR B 318 ARG 0.006 0.001 ARG B 489 Details of bonding type rmsd link_NAG-ASN : bond 0.01026 ( 5) link_NAG-ASN : angle 2.54355 ( 15) link_BETA1-4 : bond 0.00743 ( 5) link_BETA1-4 : angle 3.19998 ( 15) hydrogen bonds : bond 0.04117 ( 244) hydrogen bonds : angle 7.12658 ( 632) SS BOND : bond 0.00370 ( 36) SS BOND : angle 1.34922 ( 72) covalent geometry : bond 0.00488 (12599) covalent geometry : angle 0.78706 (17122) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 91 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.1615 (OUTLIER) cc_final: 0.0173 (mt) REVERT: A 121 GLU cc_start: 0.3592 (mp0) cc_final: 0.2633 (tt0) REVERT: A 195 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6798 (mp) REVERT: A 208 ARG cc_start: 0.6714 (OUTLIER) cc_final: 0.6380 (mmp80) REVERT: A 489 MET cc_start: 0.7726 (ppp) cc_final: 0.7395 (ppp) REVERT: A 549 MET cc_start: 0.4208 (tpt) cc_final: 0.3986 (tpt) REVERT: A 681 GLU cc_start: 0.3277 (OUTLIER) cc_final: 0.2830 (mt-10) REVERT: A 709 ASN cc_start: 0.2066 (m-40) cc_final: 0.1820 (p0) REVERT: A 827 PHE cc_start: 0.6402 (OUTLIER) cc_final: 0.5205 (m-80) REVERT: A 902 MET cc_start: 0.6917 (pmm) cc_final: 0.5077 (tmm) REVERT: B 205 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6347 (mp0) REVERT: B 344 ILE cc_start: 0.5093 (OUTLIER) cc_final: 0.4325 (mt) REVERT: B 520 TYR cc_start: 0.1250 (m-10) cc_final: 0.1019 (p90) REVERT: B 553 TRP cc_start: 0.4696 (m100) cc_final: 0.4118 (m100) REVERT: B 557 TYR cc_start: 0.5399 (t80) cc_final: 0.4948 (t80) outliers start: 55 outliers final: 30 residues processed: 140 average time/residue: 0.2170 time to fit residues: 46.2168 Evaluate side-chains 123 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 86 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 681 GLU Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 827 PHE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 621 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 54 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 141 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 138 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 107 optimal weight: 0.0770 chunk 73 optimal weight: 0.8980 chunk 1 optimal weight: 0.0470 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN B 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.232382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.195242 restraints weight = 51363.171| |-----------------------------------------------------------------------------| r_work (start): 0.4559 rms_B_bonded: 4.23 r_work: 0.4041 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4033 r_free = 0.4033 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4034 r_free = 0.4034 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| r_final: 0.4034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12645 Z= 0.143 Angle : 0.724 10.797 17224 Z= 0.361 Chirality : 0.047 0.364 1922 Planarity : 0.005 0.067 2259 Dihedral : 6.479 59.934 1937 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.38 % Favored : 91.37 % Rotamer: Outliers : 2.94 % Allowed : 19.19 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.20), residues: 1587 helix: -1.61 (0.45), residues: 121 sheet: -1.07 (0.24), residues: 456 loop : -1.74 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 235 HIS 0.004 0.001 HIS A 26 PHE 0.021 0.002 PHE A 87 TYR 0.025 0.002 TYR B 318 ARG 0.005 0.000 ARG B 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00681 ( 5) link_NAG-ASN : angle 2.13709 ( 15) link_BETA1-4 : bond 0.00770 ( 5) link_BETA1-4 : angle 2.82405 ( 15) hydrogen bonds : bond 0.03234 ( 244) hydrogen bonds : angle 6.65077 ( 632) SS BOND : bond 0.00325 ( 36) SS BOND : angle 1.20627 ( 72) covalent geometry : bond 0.00328 (12599) covalent geometry : angle 0.71436 (17122) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 94 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.1535 (OUTLIER) cc_final: 0.0330 (mt) REVERT: A 121 GLU cc_start: 0.3566 (mp0) cc_final: 0.2628 (tt0) REVERT: A 208 ARG cc_start: 0.6646 (OUTLIER) cc_final: 0.6305 (mmp80) REVERT: A 489 MET cc_start: 0.7831 (ppp) cc_final: 0.7441 (ppp) REVERT: A 681 GLU cc_start: 0.2994 (OUTLIER) cc_final: 0.2508 (mt-10) REVERT: A 709 ASN cc_start: 0.2255 (m-40) cc_final: 0.1995 (p0) REVERT: A 827 PHE cc_start: 0.6545 (OUTLIER) cc_final: 0.5456 (m-80) REVERT: A 902 MET cc_start: 0.6873 (pmm) cc_final: 0.5013 (tmm) REVERT: B 120 LEU cc_start: 0.6520 (OUTLIER) cc_final: 0.6031 (mt) REVERT: B 180 MET cc_start: 0.7073 (mpp) cc_final: 0.6861 (mpt) REVERT: B 205 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6302 (mp0) REVERT: B 520 TYR cc_start: 0.1063 (m-10) cc_final: 0.0757 (p90) REVERT: B 553 TRP cc_start: 0.4718 (m100) cc_final: 0.4184 (m100) REVERT: B 557 TYR cc_start: 0.5473 (t80) cc_final: 0.4902 (t80) REVERT: B 568 MET cc_start: 0.4722 (mtp) cc_final: 0.4485 (mtp) outliers start: 39 outliers final: 22 residues processed: 127 average time/residue: 0.2316 time to fit residues: 44.9048 Evaluate side-chains 110 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 681 GLU Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 827 PHE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 178 TYR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 621 ASP Chi-restraints excluded: chain B residue 653 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 59 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 108 optimal weight: 0.0980 chunk 157 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 78 optimal weight: 0.0470 chunk 41 optimal weight: 0.0980 chunk 105 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN B 539 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4897 r_free = 0.4897 target = 0.232217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.194934 restraints weight = 47093.803| |-----------------------------------------------------------------------------| r_work (start): 0.4560 rms_B_bonded: 4.14 r_work: 0.4043 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4034 r_free = 0.4034 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4035 r_free = 0.4035 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| r_final: 0.4035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12645 Z= 0.142 Angle : 0.710 10.577 17224 Z= 0.351 Chirality : 0.046 0.324 1922 Planarity : 0.005 0.066 2259 Dihedral : 5.938 54.107 1929 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.88 % Favored : 90.86 % Rotamer: Outliers : 3.16 % Allowed : 19.49 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.20), residues: 1587 helix: -1.41 (0.46), residues: 121 sheet: -0.93 (0.24), residues: 448 loop : -1.69 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 235 HIS 0.005 0.001 HIS A 26 PHE 0.015 0.002 PHE B 431 TYR 0.042 0.002 TYR A 380 ARG 0.004 0.000 ARG B 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00656 ( 5) link_NAG-ASN : angle 1.96574 ( 15) link_BETA1-4 : bond 0.00770 ( 5) link_BETA1-4 : angle 2.67012 ( 15) hydrogen bonds : bond 0.03187 ( 244) hydrogen bonds : angle 6.41608 ( 632) SS BOND : bond 0.00287 ( 36) SS BOND : angle 1.25583 ( 72) covalent geometry : bond 0.00326 (12599) covalent geometry : angle 0.70077 (17122) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 91 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.1199 (OUTLIER) cc_final: -0.0116 (mt) REVERT: A 121 GLU cc_start: 0.3431 (mp0) cc_final: 0.2657 (tt0) REVERT: A 195 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6650 (mp) REVERT: A 208 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.6338 (mmp80) REVERT: A 489 MET cc_start: 0.7810 (ppp) cc_final: 0.7440 (ppp) REVERT: A 681 GLU cc_start: 0.2651 (OUTLIER) cc_final: 0.2254 (mt-10) REVERT: A 827 PHE cc_start: 0.6684 (OUTLIER) cc_final: 0.5654 (m-80) REVERT: A 902 MET cc_start: 0.6772 (pmm) cc_final: 0.5021 (tmm) REVERT: B 22 MET cc_start: 0.5796 (tpt) cc_final: 0.5246 (mpp) REVERT: B 106 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7429 (mp10) REVERT: B 120 LEU cc_start: 0.6366 (OUTLIER) cc_final: 0.6046 (mt) REVERT: B 180 MET cc_start: 0.6989 (mpp) cc_final: 0.6569 (mpp) REVERT: B 205 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6322 (mp0) REVERT: B 431 PHE cc_start: 0.5298 (m-10) cc_final: 0.4785 (m-10) REVERT: B 520 TYR cc_start: 0.1025 (m-10) cc_final: 0.0757 (p90) REVERT: B 553 TRP cc_start: 0.4610 (m100) cc_final: 0.4164 (m100) REVERT: B 557 TYR cc_start: 0.5476 (t80) cc_final: 0.4881 (t80) REVERT: B 568 MET cc_start: 0.4981 (mtp) cc_final: 0.4714 (mtp) outliers start: 42 outliers final: 27 residues processed: 129 average time/residue: 0.2398 time to fit residues: 46.6214 Evaluate side-chains 119 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 84 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 681 GLU Chi-restraints excluded: chain A residue 827 PHE Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 621 ASP Chi-restraints excluded: chain B residue 653 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 104 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 85 optimal weight: 20.0000 chunk 27 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 0.0020 chunk 80 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.232068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.199226 restraints weight = 63751.008| |-----------------------------------------------------------------------------| r_work (start): 0.4602 rms_B_bonded: 4.40 r_work (final): 0.4602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4602 r_free = 0.4602 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4600 r_free = 0.4600 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 49 | |-----------------------------------------------------------------------------| r_final: 0.4600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5480 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12645 Z= 0.140 Angle : 0.704 10.823 17224 Z= 0.350 Chirality : 0.046 0.318 1922 Planarity : 0.005 0.066 2259 Dihedral : 5.821 55.548 1929 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.50 % Favored : 91.24 % Rotamer: Outliers : 2.94 % Allowed : 20.22 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.21), residues: 1587 helix: -1.33 (0.47), residues: 121 sheet: -0.89 (0.24), residues: 448 loop : -1.63 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 235 HIS 0.004 0.001 HIS A 26 PHE 0.021 0.002 PHE A 558 TYR 0.024 0.002 TYR A 380 ARG 0.006 0.000 ARG B 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00601 ( 5) link_NAG-ASN : angle 1.89840 ( 15) link_BETA1-4 : bond 0.00744 ( 5) link_BETA1-4 : angle 2.56398 ( 15) hydrogen bonds : bond 0.03078 ( 244) hydrogen bonds : angle 6.27597 ( 632) SS BOND : bond 0.00321 ( 36) SS BOND : angle 1.24846 ( 72) covalent geometry : bond 0.00322 (12599) covalent geometry : angle 0.69517 (17122) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 92 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.0856 (OUTLIER) cc_final: -0.0480 (mp) REVERT: A 121 GLU cc_start: 0.3254 (mp0) cc_final: 0.2554 (tt0) REVERT: A 195 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6399 (mp) REVERT: A 208 ARG cc_start: 0.6441 (OUTLIER) cc_final: 0.6140 (mmp80) REVERT: A 315 GLU cc_start: 0.5354 (OUTLIER) cc_final: 0.4335 (pt0) REVERT: A 479 LYS cc_start: 0.4185 (tptt) cc_final: 0.3655 (tppt) REVERT: A 681 GLU cc_start: 0.2886 (OUTLIER) cc_final: 0.2432 (mt-10) REVERT: A 827 PHE cc_start: 0.4434 (OUTLIER) cc_final: 0.3475 (m-80) REVERT: A 902 MET cc_start: 0.6151 (pmm) cc_final: 0.5225 (tmm) REVERT: B 120 LEU cc_start: 0.5921 (OUTLIER) cc_final: 0.5712 (mt) REVERT: B 205 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6704 (mp0) outliers start: 39 outliers final: 27 residues processed: 127 average time/residue: 0.2252 time to fit residues: 43.5805 Evaluate side-chains 118 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 83 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 681 GLU Chi-restraints excluded: chain A residue 827 PHE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 178 TYR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 621 ASP Chi-restraints excluded: chain B residue 653 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 14 optimal weight: 0.0020 chunk 101 optimal weight: 0.0570 chunk 9 optimal weight: 0.5980 chunk 79 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 149 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 145 optimal weight: 6.9990 overall best weight: 0.2906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 ASN B 571 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.233444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.197427 restraints weight = 52744.075| |-----------------------------------------------------------------------------| r_work (start): 0.4587 rms_B_bonded: 4.22 r_work (final): 0.4587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4587 r_free = 0.4587 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 49 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4586 r_free = 0.4586 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| r_final: 0.4586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5513 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12645 Z= 0.125 Angle : 0.691 11.037 17224 Z= 0.340 Chirality : 0.045 0.308 1922 Planarity : 0.005 0.064 2259 Dihedral : 5.731 56.374 1929 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.93 % Favored : 91.81 % Rotamer: Outliers : 2.79 % Allowed : 20.51 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.21), residues: 1587 helix: -1.23 (0.47), residues: 121 sheet: -0.85 (0.24), residues: 451 loop : -1.59 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 553 HIS 0.004 0.001 HIS A 26 PHE 0.014 0.001 PHE B 431 TYR 0.027 0.001 TYR B 557 ARG 0.007 0.000 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00551 ( 5) link_NAG-ASN : angle 1.73687 ( 15) link_BETA1-4 : bond 0.00754 ( 5) link_BETA1-4 : angle 2.43894 ( 15) hydrogen bonds : bond 0.02905 ( 244) hydrogen bonds : angle 6.12485 ( 632) SS BOND : bond 0.00378 ( 36) SS BOND : angle 1.21589 ( 72) covalent geometry : bond 0.00284 (12599) covalent geometry : angle 0.68269 (17122) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 88 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.0684 (OUTLIER) cc_final: -0.0710 (mp) REVERT: A 121 GLU cc_start: 0.3273 (mp0) cc_final: 0.3071 (tt0) REVERT: A 208 ARG cc_start: 0.6483 (OUTLIER) cc_final: 0.6127 (mmp80) REVERT: A 314 MET cc_start: 0.6208 (mtm) cc_final: 0.6004 (mtp) REVERT: A 315 GLU cc_start: 0.5332 (OUTLIER) cc_final: 0.4408 (pt0) REVERT: A 479 LYS cc_start: 0.4173 (tptt) cc_final: 0.3647 (tppt) REVERT: A 681 GLU cc_start: 0.2633 (OUTLIER) cc_final: 0.2224 (mt-10) REVERT: A 827 PHE cc_start: 0.4312 (OUTLIER) cc_final: 0.3402 (m-80) REVERT: A 902 MET cc_start: 0.6149 (pmm) cc_final: 0.5262 (tmm) outliers start: 37 outliers final: 25 residues processed: 120 average time/residue: 0.2293 time to fit residues: 41.5628 Evaluate side-chains 110 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 681 GLU Chi-restraints excluded: chain A residue 827 PHE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 621 ASP Chi-restraints excluded: chain B residue 653 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 96 optimal weight: 30.0000 chunk 127 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.227313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.189803 restraints weight = 44673.106| |-----------------------------------------------------------------------------| r_work (start): 0.4505 rms_B_bonded: 4.00 r_work: 0.3975 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3959 r_free = 0.3959 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3958 r_free = 0.3958 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| r_final: 0.3958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 12645 Z= 0.252 Angle : 0.815 10.441 17224 Z= 0.411 Chirality : 0.049 0.305 1922 Planarity : 0.006 0.057 2259 Dihedral : 6.260 57.305 1929 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.22 % Favored : 89.53 % Rotamer: Outliers : 2.72 % Allowed : 20.66 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.20), residues: 1587 helix: -1.67 (0.44), residues: 121 sheet: -1.14 (0.24), residues: 451 loop : -1.76 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 553 HIS 0.005 0.001 HIS B 192 PHE 0.022 0.003 PHE B 203 TYR 0.042 0.003 TYR A 380 ARG 0.007 0.001 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00658 ( 5) link_NAG-ASN : angle 2.08292 ( 15) link_BETA1-4 : bond 0.00702 ( 5) link_BETA1-4 : angle 2.77253 ( 15) hydrogen bonds : bond 0.04110 ( 244) hydrogen bonds : angle 6.52484 ( 632) SS BOND : bond 0.00402 ( 36) SS BOND : angle 1.62066 ( 72) covalent geometry : bond 0.00592 (12599) covalent geometry : angle 0.80404 (17122) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 82 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.6386 (OUTLIER) cc_final: 0.6124 (pp) REVERT: A 121 GLU cc_start: 0.3667 (mp0) cc_final: 0.3124 (tt0) REVERT: A 142 GLU cc_start: 0.5850 (mp0) cc_final: 0.4784 (tt0) REVERT: A 162 TRP cc_start: 0.3887 (t-100) cc_final: 0.3624 (t-100) REVERT: A 195 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6807 (mp) REVERT: A 208 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.6503 (mmp80) REVERT: A 479 LYS cc_start: 0.5034 (tptt) cc_final: 0.4049 (tppt) REVERT: A 558 PHE cc_start: 0.5669 (p90) cc_final: 0.5317 (p90) REVERT: A 681 GLU cc_start: 0.2565 (OUTLIER) cc_final: 0.2087 (mt-10) REVERT: A 827 PHE cc_start: 0.6633 (OUTLIER) cc_final: 0.5661 (m-80) REVERT: A 902 MET cc_start: 0.6798 (pmm) cc_final: 0.5129 (tmm) REVERT: B 444 ASN cc_start: 0.7309 (m-40) cc_final: 0.7091 (m110) REVERT: B 568 MET cc_start: 0.4772 (mtp) cc_final: 0.4546 (mtp) outliers start: 36 outliers final: 28 residues processed: 115 average time/residue: 0.2376 time to fit residues: 41.2048 Evaluate side-chains 111 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 78 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 681 GLU Chi-restraints excluded: chain A residue 827 PHE Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 621 ASP Chi-restraints excluded: chain B residue 653 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 147 optimal weight: 0.0970 chunk 79 optimal weight: 0.0670 chunk 78 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 145 optimal weight: 6.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.231377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.197717 restraints weight = 54504.026| |-----------------------------------------------------------------------------| r_work (start): 0.4591 rms_B_bonded: 4.08 r_work: 0.4056 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4059 r_free = 0.4059 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4058 r_free = 0.4058 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.4058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12645 Z= 0.138 Angle : 0.711 10.470 17224 Z= 0.352 Chirality : 0.046 0.296 1922 Planarity : 0.005 0.045 2259 Dihedral : 5.886 58.665 1929 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.80 % Favored : 91.94 % Rotamer: Outliers : 2.21 % Allowed : 21.40 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.21), residues: 1587 helix: -1.45 (0.46), residues: 122 sheet: -0.95 (0.25), residues: 444 loop : -1.62 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 553 HIS 0.005 0.001 HIS A 26 PHE 0.020 0.002 PHE A 558 TYR 0.039 0.002 TYR A 380 ARG 0.005 0.000 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00540 ( 5) link_NAG-ASN : angle 1.72397 ( 15) link_BETA1-4 : bond 0.00773 ( 5) link_BETA1-4 : angle 2.42604 ( 15) hydrogen bonds : bond 0.03148 ( 244) hydrogen bonds : angle 6.13843 ( 632) SS BOND : bond 0.00290 ( 36) SS BOND : angle 1.26012 ( 72) covalent geometry : bond 0.00321 (12599) covalent geometry : angle 0.70267 (17122) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.6225 (OUTLIER) cc_final: 0.5990 (pp) REVERT: A 121 GLU cc_start: 0.3537 (mp0) cc_final: 0.3066 (tt0) REVERT: A 162 TRP cc_start: 0.3963 (t-100) cc_final: 0.3685 (t-100) REVERT: A 208 ARG cc_start: 0.6767 (OUTLIER) cc_final: 0.6351 (mmp80) REVERT: A 315 GLU cc_start: 0.5425 (mt-10) cc_final: 0.4616 (pt0) REVERT: A 479 LYS cc_start: 0.4996 (tptt) cc_final: 0.3946 (tppt) REVERT: A 681 GLU cc_start: 0.2494 (OUTLIER) cc_final: 0.2013 (mt-10) REVERT: A 827 PHE cc_start: 0.6552 (OUTLIER) cc_final: 0.5570 (m-80) REVERT: A 902 MET cc_start: 0.6759 (pmm) cc_final: 0.5276 (tmm) REVERT: B 444 ASN cc_start: 0.7201 (m-40) cc_final: 0.6988 (m110) REVERT: B 568 MET cc_start: 0.4957 (mtp) cc_final: 0.4686 (mtp) outliers start: 29 outliers final: 24 residues processed: 110 average time/residue: 0.2280 time to fit residues: 38.3155 Evaluate side-chains 108 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 681 GLU Chi-restraints excluded: chain A residue 827 PHE Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 621 ASP Chi-restraints excluded: chain B residue 653 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 97 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 89 optimal weight: 20.0000 chunk 62 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 94 optimal weight: 30.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** 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 = 0.4990 r_free = 0.4990 target = 0.235033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.205336 restraints weight = 52872.462| |-----------------------------------------------------------------------------| r_work (start): 0.4722 rms_B_bonded: 3.91 r_work (final): 0.4722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4707 r_free = 0.4707 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4705 r_free = 0.4705 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 49 | |-----------------------------------------------------------------------------| r_final: 0.4705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5523 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12645 Z= 0.164 Angle : 0.730 10.195 17224 Z= 0.362 Chirality : 0.046 0.287 1922 Planarity : 0.005 0.046 2259 Dihedral : 5.913 59.350 1929 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.76 % Favored : 90.99 % Rotamer: Outliers : 2.21 % Allowed : 21.47 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.21), residues: 1587 helix: -1.46 (0.46), residues: 122 sheet: -0.95 (0.25), residues: 440 loop : -1.63 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 553 HIS 0.013 0.001 HIS B 509 PHE 0.014 0.002 PHE B 188 TYR 0.039 0.002 TYR A 380 ARG 0.006 0.001 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00571 ( 5) link_NAG-ASN : angle 1.76787 ( 15) link_BETA1-4 : bond 0.00696 ( 5) link_BETA1-4 : angle 2.48944 ( 15) hydrogen bonds : bond 0.03265 ( 244) hydrogen bonds : angle 6.16799 ( 632) SS BOND : bond 0.00316 ( 36) SS BOND : angle 1.35614 ( 72) covalent geometry : bond 0.00384 (12599) covalent geometry : angle 0.72098 (17122) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6650.57 seconds wall clock time: 115 minutes 21.62 seconds (6921.62 seconds total)