Starting phenix.real_space_refine on Fri Jul 3 05:36:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gce_29932/07_2026/8gce_29932.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gce_29932/07_2026/8gce_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 { model { file = "/net/cci-nas-00/data/ceres_data/8gce_29932/07_2026/8gce_29932.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gce_29932/07_2026/8gce_29932.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gce_29932/07_2026/8gce_29932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gce_29932/07_2026/8gce_29932.map" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 28 Ad-hoc single atom residues: {' CA': 4} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 4 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, 1 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 4.01, per 1000 atoms: 0.32 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: 0.76 Conformation dependent library (CDL) restraints added in 873.3 milliseconds 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: 0.41 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: 2.26 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 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: 2.390 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: 0.030 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.160 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5692 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 : 31.94 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.038 0.001 ARG A 661 TYR 0.029 0.002 TYR B 164 PHE 0.037 0.002 PHE A 669 TRP 0.022 0.002 TRP A 113 HIS 0.007 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00693 / 0.41 (12599) covalent geometry : angle 1.15296 / 0.66 (17122) SS BOND : bond 0.00443 / 0.25 ( 36) SS BOND : angle 1.62065 / 1.07 ( 72) hydrogen bonds : bond 0.28179 / 17.98 ( 244) hydrogen bonds : angle 11.08730 / 7.45 ( 632) link_BETA1-4 : bond 0.00816 / 0.43 ( 5) link_BETA1-4 : angle 4.24233 / 2.48 ( 15) link_NAG-ASN : bond 0.01894 / 1.07 ( 5) link_NAG-ASN : angle 3.50567 / 2.03 ( 15) *********************** 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 : 0.469 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: 0.4453 (m170) REVERT: A 121 GLU cc_start: 0.2824 (mp0) cc_final: 0.2210 (tt0) REVERT: A 124 LYS cc_start: 0.2962 (mtmm) cc_final: 0.2598 (mtmm) REVERT: A 164 LYS cc_start: 0.5149 (pttt) cc_final: 0.4629 (pttm) REVERT: A 449 ARG cc_start: 0.5775 (mpp80) cc_final: 0.4963 (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: 0.3339 (mmt) REVERT: A 691 ASN cc_start: 0.7019 (OUTLIER) cc_final: 0.6487 (m110) REVERT: A 835 LEU cc_start: 0.1899 (OUTLIER) cc_final: 0.0927 (mt) REVERT: A 837 VAL cc_start: 0.1859 (OUTLIER) cc_final: 0.1242 (m) outliers start: 45 outliers final: 17 residues processed: 202 average time/residue: 0.1181 time to fit residues: 33.7048 Evaluate side-chains 114 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.0980 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 B 497 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.234354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.197743 restraints weight = 44142.858| |-----------------------------------------------------------------------------| r_work (start): 0.4592 rms_B_bonded: 4.16 r_work: 0.4126 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4107 r_free = 0.4107 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4107 r_free = 0.4107 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (15 function evaluations) r_final: 0.4107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 12645 Z= 0.184 Angle : 0.865 11.883 17224 Z= 0.430 Chirality : 0.051 0.512 1922 Planarity : 0.005 0.058 2259 Dihedral : 9.860 83.182 1966 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.93 % Favored : 91.75 % Rotamer: Outliers : 2.65 % Allowed : 19.26 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.20), residues: 1587 helix: -1.97 (0.44), residues: 122 sheet: -0.98 (0.25), residues: 442 loop : -1.81 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 661 TYR 0.026 0.002 TYR A 380 PHE 0.033 0.002 PHE A 669 TRP 0.018 0.002 TRP B 553 HIS 0.005 0.001 HIS B 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (12599) covalent geometry : angle 0.84345 / 0.42 (17122) SS BOND : bond 0.00431 / 0.20 ( 36) SS BOND : angle 1.61495 / 1.21 ( 72) hydrogen bonds : bond 0.05172 / 3.31 ( 244) hydrogen bonds : angle 8.11035 / 5.48 ( 632) link_BETA1-4 : bond 0.01110 / 0.59 ( 5) link_BETA1-4 : angle 3.76429 / 2.42 ( 15) link_NAG-ASN : bond 0.00960 / 0.56 ( 5) link_NAG-ASN : angle 4.47093 / 2.95 ( 15) *********************** 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 148 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLN cc_start: 0.7545 (mt0) cc_final: 0.7182 (tt0) REVERT: A 121 GLU cc_start: 0.2884 (mp0) cc_final: 0.2474 (tt0) REVERT: A 520 ARG cc_start: 0.5844 (mmt180) cc_final: 0.5639 (mpt-90) REVERT: A 667 GLU cc_start: 0.4439 (OUTLIER) cc_final: 0.3711 (mm-30) REVERT: A 681 GLU cc_start: 0.3192 (OUTLIER) cc_final: 0.2955 (mp0) REVERT: A 895 MET cc_start: -0.0854 (ttt) cc_final: -0.1368 (ttt) REVERT: A 902 MET cc_start: 0.6718 (pmm) cc_final: 0.4838 (tmm) REVERT: A 931 ASN cc_start: 0.4465 (p0) cc_final: 0.4146 (t0) REVERT: B 377 ASN cc_start: 0.7095 (m-40) cc_final: 0.6745 (t0) REVERT: B 520 TYR cc_start: 0.4007 (m-80) cc_final: 0.3759 (m-10) REVERT: B 582 GLU cc_start: 0.6707 (tp30) cc_final: 0.6110 (tm-30) outliers start: 35 outliers final: 14 residues processed: 137 average time/residue: 0.0992 time to fit residues: 20.2939 Evaluate side-chains 111 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 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 835 LEU Chi-restraints excluded: chain B residue 53 SER 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 379 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 81 optimal weight: 30.0000 chunk 78 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 106 optimal weight: 0.4980 chunk 105 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 665 ASN A 808 GLN 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 = 0.233278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.200819 restraints weight = 60985.278| |-----------------------------------------------------------------------------| r_work (start): 0.4615 rms_B_bonded: 4.41 r_work (final): 0.4615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4610 r_free = 0.4610 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 = 0.4609 r_free = 0.4609 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (7 function evaluations) r_final: 0.4609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5579 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12645 Z= 0.178 Angle : 0.784 10.290 17224 Z= 0.390 Chirality : 0.049 0.315 1922 Planarity : 0.005 0.075 2259 Dihedral : 7.936 60.786 1943 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.01 % Favored : 90.67 % Rotamer: Outliers : 2.65 % Allowed : 18.82 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.20), residues: 1587 helix: -1.79 (0.45), residues: 116 sheet: -1.01 (0.24), residues: 446 loop : -1.79 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 91 TYR 0.017 0.002 TYR A 190 PHE 0.025 0.002 PHE A 669 TRP 0.015 0.002 TRP B 553 HIS 0.005 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (12599) covalent geometry : angle 0.76809 / 0.39 (17122) SS BOND : bond 0.00414 / 0.19 ( 36) SS BOND : angle 1.36966 / 0.96 ( 72) hydrogen bonds : bond 0.04248 / 2.72 ( 244) hydrogen bonds : angle 7.33333 / 4.95 ( 632) link_BETA1-4 : bond 0.00963 / 0.52 ( 5) link_BETA1-4 : angle 3.19060 / 1.87 ( 15) link_NAG-ASN : bond 0.00442 / 0.24 ( 5) link_NAG-ASN : angle 3.63663 / 2.22 ( 15) *********************** 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 129 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLN cc_start: 0.6856 (mt0) cc_final: 0.6556 (tt0) REVERT: A 315 GLU cc_start: 0.5430 (mt-10) cc_final: 0.3481 (tt0) REVERT: A 667 GLU cc_start: 0.4973 (OUTLIER) cc_final: 0.3659 (mm-30) REVERT: A 681 GLU cc_start: 0.3315 (OUTLIER) cc_final: 0.3044 (mt-10) REVERT: A 902 MET cc_start: 0.6599 (pmm) cc_final: 0.5297 (tmm) REVERT: B 568 MET cc_start: 0.4277 (OUTLIER) cc_final: 0.4036 (mtp) outliers start: 35 outliers final: 21 residues processed: 126 average time/residue: 0.0944 time to fit residues: 18.0585 Evaluate side-chains 102 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 350 THR 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 681 GLU Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 315 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 568 MET Chi-restraints excluded: chain B residue 653 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 83 optimal weight: 9.9990 chunk 132 optimal weight: 0.7980 chunk 138 optimal weight: 8.9990 chunk 67 optimal weight: 0.0040 chunk 140 optimal weight: 10.0000 chunk 7 optimal weight: 0.4980 chunk 148 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 71 optimal weight: 20.0000 chunk 31 optimal weight: 0.7980 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 GLN ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.232553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.197621 restraints weight = 55415.714| |-----------------------------------------------------------------------------| r_work (start): 0.4579 rms_B_bonded: 4.11 r_work: 0.4065 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.4065 ------------------------------------------------------------------------------- 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: 34 | |-----------------------------------------------------------------------------| |-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: 34 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (12 function evaluations) r_final: 0.4058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12645 Z= 0.164 Angle : 0.763 9.911 17224 Z= 0.377 Chirality : 0.048 0.485 1922 Planarity : 0.005 0.068 2259 Dihedral : 7.048 59.667 1938 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.69 % Favored : 90.99 % Rotamer: Outliers : 3.16 % Allowed : 18.90 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.20), residues: 1587 helix: -1.59 (0.47), residues: 115 sheet: -0.96 (0.24), residues: 453 loop : -1.78 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 214 TYR 0.032 0.002 TYR B 557 PHE 0.023 0.002 PHE A 669 TRP 0.013 0.002 TRP B 553 HIS 0.004 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (12599) covalent geometry : angle 0.75177 / 0.37 (17122) SS BOND : bond 0.00358 / 0.19 ( 36) SS BOND : angle 1.29839 / 0.94 ( 72) hydrogen bonds : bond 0.03711 / 2.41 ( 244) hydrogen bonds : angle 6.99662 / 4.72 ( 632) link_BETA1-4 : bond 0.00858 / 0.47 ( 5) link_BETA1-4 : angle 3.08679 / 1.81 ( 15) link_NAG-ASN : bond 0.00952 / 0.50 ( 5) link_NAG-ASN : angle 2.45186 / 1.58 ( 15) *********************** 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 133 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 91 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6666 (mp) REVERT: A 315 GLU cc_start: 0.5776 (mt-10) cc_final: 0.3763 (tt0) REVERT: A 549 MET cc_start: 0.4117 (tpt) cc_final: 0.3909 (tpt) REVERT: A 681 GLU cc_start: 0.3289 (OUTLIER) cc_final: 0.2878 (mt-10) REVERT: A 827 PHE cc_start: 0.6368 (OUTLIER) cc_final: 0.5146 (m-80) REVERT: A 902 MET cc_start: 0.6926 (pmm) cc_final: 0.5072 (tmm) REVERT: B 120 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.6223 (mt) REVERT: B 180 MET cc_start: 0.6856 (mpp) cc_final: 0.6625 (mpp) REVERT: B 377 ASN cc_start: 0.7108 (m-40) cc_final: 0.6813 (t0) outliers start: 42 outliers final: 28 residues processed: 129 average time/residue: 0.0902 time to fit residues: 18.0811 Evaluate side-chains 116 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 350 THR 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 114 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 315 VAL 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 587 VAL Chi-restraints excluded: chain B residue 621 ASP Chi-restraints excluded: chain B residue 653 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 139 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 153 optimal weight: 20.0000 chunk 53 optimal weight: 0.7980 chunk 84 optimal weight: 20.0000 chunk 128 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 109 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 665 ASN A 808 GLN ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.233021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.197349 restraints weight = 53729.590| |-----------------------------------------------------------------------------| r_work (start): 0.4576 rms_B_bonded: 4.09 r_work: 0.4065 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4060 r_free = 0.4060 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4061 r_free = 0.4061 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (15 function evaluations) r_final: 0.4061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12645 Z= 0.157 Angle : 0.738 12.146 17224 Z= 0.367 Chirality : 0.047 0.394 1922 Planarity : 0.005 0.068 2259 Dihedral : 6.330 58.225 1936 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.57 % Favored : 91.12 % Rotamer: Outliers : 2.79 % Allowed : 18.90 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.20), residues: 1587 helix: -1.42 (0.48), residues: 115 sheet: -0.99 (0.24), residues: 447 loop : -1.71 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 91 TYR 0.053 0.002 TYR A 380 PHE 0.018 0.002 PHE A 87 TRP 0.012 0.002 TRP A 235 HIS 0.003 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (12599) covalent geometry : angle 0.72802 / 0.36 (17122) SS BOND : bond 0.00366 / 0.16 ( 36) SS BOND : angle 1.24468 / 0.76 ( 72) hydrogen bonds : bond 0.03418 / 2.19 ( 244) hydrogen bonds : angle 6.61872 / 4.46 ( 632) link_BETA1-4 : bond 0.00788 / 0.43 ( 5) link_BETA1-4 : angle 2.84561 / 1.70 ( 15) link_NAG-ASN : bond 0.00683 / 0.36 ( 5) link_NAG-ASN : angle 2.09019 / 1.30 ( 15) *********************** 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 126 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6716 (mp) REVERT: A 208 ARG cc_start: 0.6511 (OUTLIER) cc_final: 0.6195 (mmp80) REVERT: A 315 GLU cc_start: 0.5687 (mt-10) cc_final: 0.3695 (tt0) REVERT: A 380 TYR cc_start: 0.7072 (m-10) cc_final: 0.6828 (m-10) REVERT: A 427 ILE cc_start: 0.6958 (OUTLIER) cc_final: 0.6130 (tt) REVERT: A 489 MET cc_start: 0.7531 (ppp) cc_final: 0.7231 (ppp) REVERT: A 681 GLU cc_start: 0.2923 (OUTLIER) cc_final: 0.2424 (mt-10) REVERT: A 827 PHE cc_start: 0.6581 (OUTLIER) cc_final: 0.5487 (m-80) REVERT: A 902 MET cc_start: 0.6789 (pmm) cc_final: 0.4980 (tmm) REVERT: B 120 LEU cc_start: 0.6450 (OUTLIER) cc_final: 0.6194 (mt) outliers start: 37 outliers final: 23 residues processed: 123 average time/residue: 0.0839 time to fit residues: 15.8786 Evaluate side-chains 115 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 72 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 350 THR Chi-restraints excluded: chain A residue 427 ILE 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 178 TYR Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 312 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 140 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** B 497 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.229444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.193193 restraints weight = 52249.320| |-----------------------------------------------------------------------------| r_work (start): 0.4535 rms_B_bonded: 4.11 r_work: 0.3980 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3977 r_free = 0.3977 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3978 r_free = 0.3978 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.3978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12645 Z= 0.222 Angle : 0.805 11.122 17224 Z= 0.402 Chirality : 0.049 0.333 1922 Planarity : 0.005 0.068 2259 Dihedral : 6.233 53.869 1929 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.96 % Favored : 89.78 % Rotamer: Outliers : 2.79 % Allowed : 19.26 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.20), residues: 1587 helix: -1.63 (0.46), residues: 115 sheet: -1.10 (0.24), residues: 449 loop : -1.78 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 279 TYR 0.036 0.002 TYR B 318 PHE 0.035 0.003 PHE A 87 TRP 0.014 0.002 TRP A 260 HIS 0.005 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 (12599) covalent geometry : angle 0.79419 / 0.40 (17122) SS BOND : bond 0.00353 / 0.19 ( 36) SS BOND : angle 1.50230 / 0.87 ( 72) hydrogen bonds : bond 0.03912 / 2.55 ( 244) hydrogen bonds : angle 6.78006 / 4.55 ( 632) link_BETA1-4 : bond 0.00719 / 0.39 ( 5) link_BETA1-4 : angle 2.95433 / 1.84 ( 15) link_NAG-ASN : bond 0.00699 / 0.36 ( 5) link_NAG-ASN : angle 2.15940 / 1.29 ( 15) *********************** 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 123 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 86 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.1756 (OUTLIER) cc_final: 0.0669 (mt) REVERT: A 87 PHE cc_start: 0.6756 (m-10) cc_final: 0.6530 (m-80) REVERT: A 208 ARG cc_start: 0.6771 (OUTLIER) cc_final: 0.6475 (mmp80) REVERT: A 427 ILE cc_start: 0.7060 (OUTLIER) cc_final: 0.6254 (tt) REVERT: A 489 MET cc_start: 0.7635 (ppp) cc_final: 0.7325 (ppp) REVERT: A 681 GLU cc_start: 0.2623 (OUTLIER) cc_final: 0.2201 (mt-10) REVERT: A 827 PHE cc_start: 0.6706 (OUTLIER) cc_final: 0.5675 (m-80) REVERT: A 902 MET cc_start: 0.6665 (pmm) cc_final: 0.4969 (tmm) REVERT: B 22 MET cc_start: 0.5634 (tpt) cc_final: 0.5136 (mpp) REVERT: B 431 PHE cc_start: 0.5296 (m-10) cc_final: 0.4817 (m-10) outliers start: 37 outliers final: 26 residues processed: 121 average time/residue: 0.0883 time to fit residues: 16.2946 Evaluate side-chains 111 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 80 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 72 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 208 ARG Chi-restraints excluded: chain A residue 248 LEU 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 427 ILE Chi-restraints excluded: chain A residue 454 VAL 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 114 ILE Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 277 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 17 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 148 optimal weight: 3.9990 chunk 143 optimal weight: 0.1980 chunk 95 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.232122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.194991 restraints weight = 43562.529| |-----------------------------------------------------------------------------| r_work (start): 0.4557 rms_B_bonded: 3.96 r_work: 0.4060 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4048 r_free = 0.4048 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4049 r_free = 0.4049 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.4049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.3639 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= 0.150 Angle : 0.724 11.576 17224 Z= 0.357 Chirality : 0.046 0.320 1922 Planarity : 0.005 0.065 2259 Dihedral : 5.942 55.662 1929 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.19 % Favored : 91.50 % Rotamer: Outliers : 2.35 % Allowed : 20.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.20), residues: 1587 helix: -1.55 (0.46), residues: 121 sheet: -1.01 (0.24), residues: 447 loop : -1.69 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 724 TYR 0.027 0.002 TYR B 318 PHE 0.027 0.002 PHE A 87 TRP 0.015 0.002 TRP A 235 HIS 0.003 0.001 HIS B 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (12599) covalent geometry : angle 0.71505 / 0.36 (17122) SS BOND : bond 0.00290 / 0.15 ( 36) SS BOND : angle 1.21930 / 0.71 ( 72) hydrogen bonds : bond 0.03252 / 2.08 ( 244) hydrogen bonds : angle 6.46034 / 4.32 ( 632) link_BETA1-4 : bond 0.00787 / 0.42 ( 5) link_BETA1-4 : angle 2.58925 / 1.56 ( 15) link_NAG-ASN : bond 0.00611 / 0.32 ( 5) link_NAG-ASN : angle 1.92641 / 1.16 ( 15) *********************** 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 127 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.1625 (OUTLIER) cc_final: 0.0440 (mt) REVERT: A 124 LYS cc_start: 0.2893 (mtmm) cc_final: 0.2438 (ttmt) REVERT: A 208 ARG cc_start: 0.6628 (OUTLIER) cc_final: 0.6249 (mmp80) REVERT: A 315 GLU cc_start: 0.5594 (mt-10) cc_final: 0.3678 (tt0) REVERT: A 427 ILE cc_start: 0.6727 (OUTLIER) cc_final: 0.6213 (tt) REVERT: A 489 MET cc_start: 0.7652 (ppp) cc_final: 0.7356 (ppp) REVERT: A 491 VAL cc_start: 0.7077 (OUTLIER) cc_final: 0.6827 (p) REVERT: A 681 GLU cc_start: 0.2657 (OUTLIER) cc_final: 0.2218 (mt-10) REVERT: A 827 PHE cc_start: 0.6785 (OUTLIER) cc_final: 0.5805 (m-80) REVERT: A 902 MET cc_start: 0.6760 (pmm) cc_final: 0.5073 (tmm) REVERT: B 22 MET cc_start: 0.5816 (tpt) cc_final: 0.5297 (mpp) REVERT: B 431 PHE cc_start: 0.5466 (m-10) cc_final: 0.5067 (m-10) REVERT: B 553 TRP cc_start: 0.4534 (m100) cc_final: 0.4275 (m100) REVERT: B 568 MET cc_start: 0.4936 (mtp) cc_final: 0.4653 (mtp) outliers start: 31 outliers final: 20 residues processed: 126 average time/residue: 0.0891 time to fit residues: 17.3908 Evaluate side-chains 109 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 208 ARG Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 491 VAL 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 277 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 154 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 157 optimal weight: 0.0770 chunk 105 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 148 optimal weight: 0.0060 chunk 39 optimal weight: 1.9990 overall best weight: 0.9758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN A 722 GLN ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.230731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.195157 restraints weight = 50056.962| |-----------------------------------------------------------------------------| r_work (start): 0.4559 rms_B_bonded: 3.97 r_work: 0.4025 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4018 r_free = 0.4018 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4018 r_free = 0.4018 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (11 function evaluations) r_final: 0.4018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12645 Z= 0.172 Angle : 0.740 9.470 17224 Z= 0.369 Chirality : 0.047 0.306 1922 Planarity : 0.005 0.064 2259 Dihedral : 6.059 56.796 1929 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.03 % Favored : 89.72 % Rotamer: Outliers : 2.43 % Allowed : 20.59 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.20), residues: 1587 helix: -1.60 (0.46), residues: 121 sheet: -1.04 (0.24), residues: 442 loop : -1.75 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 214 TYR 0.029 0.002 TYR B 318 PHE 0.014 0.002 PHE B 153 TRP 0.012 0.002 TRP A 260 HIS 0.003 0.001 HIS B 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (12599) covalent geometry : angle 0.73067 / 0.37 (17122) SS BOND : bond 0.00299 / 0.15 ( 36) SS BOND : angle 1.40113 / 0.77 ( 72) hydrogen bonds : bond 0.03412 / 2.16 ( 244) hydrogen bonds : angle 6.39412 / 4.26 ( 632) link_BETA1-4 : bond 0.00774 / 0.42 ( 5) link_BETA1-4 : angle 2.60553 / 1.59 ( 15) link_NAG-ASN : bond 0.00635 / 0.34 ( 5) link_NAG-ASN : angle 1.86500 / 1.06 ( 15) *********************** 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 120 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.1883 (OUTLIER) cc_final: 0.0694 (mt) REVERT: A 163 ASP cc_start: 0.6662 (OUTLIER) cc_final: 0.5211 (t0) REVERT: A 208 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.6395 (mmp80) REVERT: A 350 THR cc_start: 0.6070 (OUTLIER) cc_final: 0.5698 (m) REVERT: A 489 MET cc_start: 0.7324 (ppp) cc_final: 0.7011 (ppp) REVERT: A 681 GLU cc_start: 0.2418 (OUTLIER) cc_final: 0.1942 (mt-10) REVERT: A 827 PHE cc_start: 0.6581 (OUTLIER) cc_final: 0.5597 (m-80) REVERT: A 902 MET cc_start: 0.6765 (pmm) cc_final: 0.5112 (tmm) REVERT: B 22 MET cc_start: 0.5693 (tpt) cc_final: 0.5195 (mpp) REVERT: B 431 PHE cc_start: 0.5542 (m-10) cc_final: 0.5069 (m-10) REVERT: B 444 ASN cc_start: 0.7185 (m-40) cc_final: 0.6951 (m110) REVERT: B 568 MET cc_start: 0.4811 (mtp) cc_final: 0.4549 (mtp) outliers start: 32 outliers final: 25 residues processed: 118 average time/residue: 0.0953 time to fit residues: 16.7878 Evaluate side-chains 114 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 83 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 163 ASP 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 307 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 427 ILE 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 205 GLU 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 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 79 optimal weight: 0.0770 chunk 86 optimal weight: 8.9990 chunk 27 optimal weight: 0.3980 chunk 33 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 71 optimal weight: 20.0000 chunk 135 optimal weight: 5.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.230951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.196238 restraints weight = 56083.923| |-----------------------------------------------------------------------------| r_work (start): 0.4567 rms_B_bonded: 4.31 r_work (final): 0.4567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4569 r_free = 0.4569 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4565 r_free = 0.4565 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 49 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (9 function evaluations) r_final: 0.4565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5690 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 12645 Z= 0.194 Angle : 0.947 59.199 17224 Z= 0.523 Chirality : 0.046 0.281 1922 Planarity : 0.005 0.062 2259 Dihedral : 6.047 56.854 1929 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.71 % Favored : 90.04 % Rotamer: Outliers : 2.57 % Allowed : 20.74 % Favored : 76.69 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.20), residues: 1587 helix: -1.59 (0.46), residues: 121 sheet: -1.05 (0.24), residues: 442 loop : -1.74 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 553 TYR 0.026 0.002 TYR B 318 PHE 0.014 0.002 PHE B 188 TRP 0.039 0.002 TRP B 553 HIS 0.003 0.001 HIS B 539 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (12599) covalent geometry : angle 0.94060 / 0.52 (17122) SS BOND : bond 0.00331 / 0.22 ( 36) SS BOND : angle 1.43091 / 0.79 ( 72) hydrogen bonds : bond 0.03386 / 2.14 ( 244) hydrogen bonds : angle 6.39208 / 4.26 ( 632) link_BETA1-4 : bond 0.00667 / 0.36 ( 5) link_BETA1-4 : angle 2.62105 / 1.60 ( 15) link_NAG-ASN : bond 0.00607 / 0.32 ( 5) link_NAG-ASN : angle 1.86307 / 1.07 ( 15) *********************** 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 116 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 82 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.1335 (OUTLIER) cc_final: 0.0425 (mt) REVERT: A 163 ASP cc_start: 0.6440 (OUTLIER) cc_final: 0.4961 (t0) REVERT: A 208 ARG cc_start: 0.6577 (OUTLIER) cc_final: 0.6251 (mmp80) REVERT: A 350 THR cc_start: 0.5809 (OUTLIER) cc_final: 0.5369 (m) REVERT: A 577 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7325 (tt0) REVERT: A 681 GLU cc_start: 0.2653 (OUTLIER) cc_final: 0.2225 (mt-10) REVERT: A 827 PHE cc_start: 0.4318 (OUTLIER) cc_final: 0.3446 (m-80) REVERT: A 902 MET cc_start: 0.6127 (pmm) cc_final: 0.5224 (tmm) outliers start: 34 outliers final: 26 residues processed: 115 average time/residue: 0.1076 time to fit residues: 19.1534 Evaluate side-chains 115 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 82 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 163 ASP Chi-restraints excluded: chain A residue 166 TYR 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 307 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 577 GLU 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 205 GLU 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 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 587 VAL 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 136 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 123 optimal weight: 0.0870 chunk 7 optimal weight: 0.3980 chunk 18 optimal weight: 0.1980 chunk 91 optimal weight: 0.0570 chunk 64 optimal weight: 6.9990 chunk 31 optimal weight: 0.0070 chunk 148 optimal weight: 0.1980 chunk 63 optimal weight: 0.1980 overall best weight: 0.1094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.230796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.196865 restraints weight = 58745.123| |-----------------------------------------------------------------------------| r_work (start): 0.4579 rms_B_bonded: 4.22 r_work (final): 0.4579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4578 r_free = 0.4578 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 = 0.4577 r_free = 0.4577 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.4577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5675 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 12645 Z= 0.195 Angle : 0.947 59.199 17224 Z= 0.524 Chirality : 0.046 0.281 1922 Planarity : 0.005 0.062 2259 Dihedral : 6.047 56.854 1929 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.71 % Favored : 90.04 % Rotamer: Outliers : 2.50 % Allowed : 20.96 % Favored : 76.54 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.20), residues: 1587 helix: -1.59 (0.46), residues: 121 sheet: -1.05 (0.24), residues: 442 loop : -1.74 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 553 TYR 0.026 0.002 TYR B 318 PHE 0.014 0.002 PHE B 188 TRP 0.039 0.002 TRP B 553 HIS 0.003 0.001 HIS B 539 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (12599) covalent geometry : angle 0.94061 / 0.52 (17122) SS BOND : bond 0.00459 / 0.25 ( 36) SS BOND : angle 1.45832 / 0.80 ( 72) hydrogen bonds : bond 0.03386 / 2.14 ( 244) hydrogen bonds : angle 6.39208 / 4.26 ( 632) link_BETA1-4 : bond 0.00667 / 0.36 ( 5) link_BETA1-4 : angle 2.62105 / 1.60 ( 15) link_NAG-ASN : bond 0.00607 / 0.32 ( 5) link_NAG-ASN : angle 1.86307 / 1.07 ( 15) ********************** 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 115 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 82 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.1354 (OUTLIER) cc_final: 0.0433 (mt) REVERT: A 163 ASP cc_start: 0.6446 (OUTLIER) cc_final: 0.4972 (t0) REVERT: A 208 ARG cc_start: 0.6607 (OUTLIER) cc_final: 0.6281 (mmp80) REVERT: A 350 THR cc_start: 0.5824 (OUTLIER) cc_final: 0.5380 (m) REVERT: A 577 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7317 (tt0) REVERT: A 681 GLU cc_start: 0.2685 (OUTLIER) cc_final: 0.2243 (mt-10) REVERT: A 827 PHE cc_start: 0.4302 (OUTLIER) cc_final: 0.3435 (m-80) REVERT: A 902 MET cc_start: 0.6130 (pmm) cc_final: 0.5229 (tmm) outliers start: 33 outliers final: 26 residues processed: 114 average time/residue: 0.1057 time to fit residues: 18.4559 Evaluate side-chains 115 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 82 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 163 ASP Chi-restraints excluded: chain A residue 166 TYR 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 307 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 577 GLU 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 205 GLU 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 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 587 VAL 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 139 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 149 optimal weight: 0.0570 chunk 89 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 69 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.230812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.193213 restraints weight = 40710.665| |-----------------------------------------------------------------------------| r_work (start): 0.4544 rms_B_bonded: 4.07 r_work: 0.4030 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4016 r_free = 0.4016 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4015 r_free = 0.4015 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (16 function evaluations) r_final: 0.4015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 12645 Z= 0.195 Angle : 0.947 59.199 17224 Z= 0.524 Chirality : 0.046 0.281 1922 Planarity : 0.005 0.062 2259 Dihedral : 6.047 56.854 1929 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.71 % Favored : 90.04 % Rotamer: Outliers : 2.50 % Allowed : 20.96 % Favored : 76.54 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.20), residues: 1587 helix: -1.59 (0.46), residues: 121 sheet: -1.05 (0.24), residues: 442 loop : -1.74 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 553 TYR 0.026 0.002 TYR B 318 PHE 0.014 0.002 PHE B 188 TRP 0.039 0.002 TRP B 553 HIS 0.003 0.001 HIS B 539 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (12599) covalent geometry : angle 0.94061 / 0.52 (17122) SS BOND : bond 0.00459 / 0.25 ( 36) SS BOND : angle 1.45832 / 0.80 ( 72) hydrogen bonds : bond 0.03386 / 2.14 ( 244) hydrogen bonds : angle 6.39208 / 4.26 ( 632) link_BETA1-4 : bond 0.00667 / 0.36 ( 5) link_BETA1-4 : angle 2.62105 / 1.60 ( 15) link_NAG-ASN : bond 0.00607 / 0.32 ( 5) link_NAG-ASN : angle 1.86307 / 1.07 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2974.39 seconds wall clock time: 51 minutes 47.00 seconds (3107.00 seconds total)