Starting phenix.real_space_refine on Sun Nov 17 00:16:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gce_29932/11_2024/8gce_29932.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gce_29932/11_2024/8gce_29932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gce_29932/11_2024/8gce_29932.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gce_29932/11_2024/8gce_29932.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gce_29932/11_2024/8gce_29932.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gce_29932/11_2024/8gce_29932.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 Mg 1 5.21 5 S 98 5.16 5 C 7697 2.51 5 N 2116 2.21 5 O 2425 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12343 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7007 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 912, 6966 Classifications: {'peptide': 912} Link IDs: {'PCIS': 2, 'PTRANS': 59, 'TRANS': 850} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 912, 6966 Classifications: {'peptide': 912} Link IDs: {'PCIS': 2, 'PTRANS': 59, 'TRANS': 850} Chain breaks: 2 bond proxies already assigned to first conformer: 7082 Chain: "B" Number of atoms: 5195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 676, 5191 Classifications: {'peptide': 676} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 643} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 676, 5191 Classifications: {'peptide': 676} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 643} Chain breaks: 2 bond proxies already assigned to first conformer: 5277 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 32 Unusual residues: {' CA': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 72 residue: pdb=" N AGLN A 177 " occ=0.51 ... (16 atoms not shown) pdb=" NE2BGLN A 177 " occ=0.49 residue: pdb=" N AARG A 276 " occ=0.92 ... (20 atoms not shown) pdb=" NH2BARG A 276 " occ=0.08 residue: pdb=" N AHIS A 587 " occ=0.40 ... (18 atoms not shown) pdb=" NE2BHIS A 587 " occ=0.60 residue: pdb=" N PRO B 605 " occ=0.71 ... (5 atoms not shown) pdb=" CD PRO B 605 " occ=0.71 residue: pdb=" N ASP B 606 " occ=0.49 ... (6 atoms not shown) pdb=" OD2 ASP B 606 " occ=0.49 residue: pdb=" N ALA B 607 " occ=0.70 ... (3 atoms not shown) pdb=" CB ALA B 607 " occ=0.70 residue: pdb=" N CYS B 608 " occ=0.50 ... (4 atoms not shown) pdb=" SG CYS B 608 " occ=0.50 residue: pdb=" N THR B 609 " occ=0.56 ... (5 atoms not shown) pdb=" CG2 THR B 609 " occ=0.56 residue: pdb=" N PHE B 610 " occ=0.93 ... (9 atoms not shown) pdb=" CZ PHE B 610 " occ=0.93 residue: pdb=" N LYS B 611 " occ=0.77 ... (7 atoms not shown) pdb=" NZ LYS B 611 " occ=0.77 residue: pdb=" N LYS B 612 " occ=0.67 ... (7 atoms not shown) pdb=" NZ LYS B 612 " occ=0.67 residue: pdb=" N GLU B 613 " occ=0.76 ... (7 atoms not shown) pdb=" OE2 GLU B 613 " occ=0.76 ... (remaining 60 not shown) Time building chain proxies: 12.99, per 1000 atoms: 1.05 Number of scatterers: 12343 At special positions: 0 Unit cell: (104.86, 123.05, 129.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 98 16.00 Mg 1 11.99 O 2425 8.00 N 2116 7.00 C 7697 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 167 " distance=2.02 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 545 " distance=2.03 Simple disulfide: pdb=" SG CYS A 602 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 674 " - pdb=" SG CYS A 687 " distance=2.04 Simple disulfide: pdb=" SG CYS A 826 " - pdb=" SG CYS A 890 " distance=2.03 Simple disulfide: pdb=" SG CYS A 880 " - pdb=" SG CYS A 885 " distance=2.03 Simple disulfide: pdb=" SG CYS B 5 " - pdb=" SG CYS B 23 " distance=2.03 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 435 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 38 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 386 " distance=2.04 Simple disulfide: pdb=" SG CYS B 406 " - pdb=" SG CYS B 433 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 448 " - pdb=" SG CYS B 460 " distance=2.03 Simple disulfide: pdb=" SG CYS B 462 " - pdb=" SG CYS B 471 " distance=2.03 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 503 " distance=2.03 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 501 " distance=2.03 Simple disulfide: pdb=" SG CYS B 495 " - pdb=" SG CYS B 506 " distance=2.03 Simple disulfide: pdb=" SG CYS B 508 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 523 " - pdb=" SG CYS B 544 " distance=2.03 Simple disulfide: pdb=" SG CYS B 528 " - pdb=" SG CYS B 542 " distance=2.04 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 547 " distance=2.03 Simple disulfide: pdb=" SG CYS B 549 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 560 " - pdb=" SG CYS B 583 " distance=2.03 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 581 " distance=2.02 Simple disulfide: pdb=" SG CYS B 575 " - pdb=" SG CYS B 586 " distance=2.03 Simple disulfide: pdb=" SG CYS B 588 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 655 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 631 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1105 " - " ASN A 15 " " NAG A1106 " - " ASN A 570 " " NAG C 1 " - " ASN B 371 " " NAG D 1 " - " ASN B 320 " " NAG E 1 " - " ASN B 99 " Time building additional restraints: 3.57 Conformation dependent library (CDL) restraints added in 3.5 seconds 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2920 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 25 sheets defined 10.2% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 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: 4.46 Time building geometry restraints manager: 4.02 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 39.770 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5559 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.167 12599 Z= 0.479 Angle : 1.153 28.849 17122 Z= 0.659 Chirality : 0.077 1.077 1922 Planarity : 0.015 0.308 2259 Dihedral : 16.738 122.547 4804 Min Nonbonded Distance : 1.584 Molprobity Statistics. All-atom Clashscore : 31.98 Ramachandran Plot: Outliers : 1.59 % Allowed : 9.64 % Favored : 88.77 % Rotamer: Outliers : 3.38 % Allowed : 17.57 % Favored : 79.04 % Cbeta Deviations : 1.03 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.20), residues: 1587 helix: -2.13 (0.43), residues: 122 sheet: -0.83 (0.26), residues: 425 loop : -1.84 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 113 HIS 0.007 0.001 HIS B 274 PHE 0.037 0.002 PHE A 669 TYR 0.029 0.002 TYR B 164 ARG 0.038 0.001 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLN cc_start: 0.7898 (mt0) cc_final: 0.7512 (tt0) REVERT: A 112 HIS cc_start: 0.4661 (m90) cc_final: 0.4455 (m170) REVERT: A 121 GLU cc_start: 0.2824 (mp0) cc_final: 0.2220 (tt0) REVERT: A 124 LYS cc_start: 0.2962 (mtmm) cc_final: 0.2582 (mtmm) REVERT: A 164 LYS cc_start: 0.5149 (pttt) cc_final: 0.4624 (pttm) REVERT: A 449 ARG cc_start: 0.5775 (mpp80) cc_final: 0.4968 (mtp180) REVERT: A 489 MET cc_start: 0.5934 (ppp) cc_final: 0.5655 (tpt) REVERT: A 660 MET cc_start: 0.4302 (mmm) cc_final: 0.3346 (mmt) REVERT: A 691 ASN cc_start: 0.7019 (OUTLIER) cc_final: 0.6490 (m110) REVERT: A 835 LEU cc_start: 0.1899 (OUTLIER) cc_final: 0.0928 (mt) REVERT: A 837 VAL cc_start: 0.1859 (OUTLIER) cc_final: 0.1241 (m) outliers start: 45 outliers final: 18 residues processed: 202 average time/residue: 0.2799 time to fit residues: 79.1602 Evaluate side-chains 115 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 PRO Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 670 GLU Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 507 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 47 optimal weight: 20.0000 chunk 75 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 ASN A 665 ASN A 808 GLN A 833 ASN B 79 GLN B 255 HIS B 319 GLN ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.127 12599 Z= 0.554 Angle : 1.038 11.319 17122 Z= 0.531 Chirality : 0.057 0.337 1922 Planarity : 0.007 0.093 2259 Dihedral : 10.181 80.642 1968 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.09 % Favored : 89.59 % Rotamer: Outliers : 4.19 % Allowed : 17.57 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.20), residues: 1587 helix: -2.80 (0.37), residues: 123 sheet: -1.28 (0.24), residues: 446 loop : -2.09 (0.18), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 553 HIS 0.011 0.002 HIS A 304 PHE 0.032 0.004 PHE B 203 TYR 0.031 0.004 TYR A 190 ARG 0.010 0.001 ARG B 150 *********************** 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 167 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 111 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ASN cc_start: 0.7042 (OUTLIER) cc_final: 0.6665 (m-40) REVERT: A 84 LEU cc_start: 0.0564 (OUTLIER) cc_final: -0.0322 (mt) REVERT: A 124 LYS cc_start: 0.3392 (mtmm) cc_final: 0.3110 (mtmm) REVERT: A 208 ARG cc_start: 0.5986 (OUTLIER) cc_final: 0.5761 (mmp80) REVERT: A 667 GLU cc_start: 0.5038 (OUTLIER) cc_final: 0.3483 (mm-30) REVERT: A 895 MET cc_start: -0.0497 (ttt) cc_final: -0.0944 (ttt) REVERT: B 304 ILE cc_start: 0.5811 (mm) cc_final: 0.5607 (mm) REVERT: B 459 VAL cc_start: 0.4609 (OUTLIER) cc_final: 0.4254 (p) outliers start: 56 outliers final: 26 residues processed: 155 average time/residue: 0.2417 time to fit residues: 55.6775 Evaluate side-chains 119 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 178 TYR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 653 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 143 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN A 808 GLN ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5661 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12599 Z= 0.270 Angle : 0.782 9.494 17122 Z= 0.396 Chirality : 0.050 0.333 1922 Planarity : 0.005 0.078 2259 Dihedral : 7.733 59.733 1939 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.95 % Favored : 90.80 % Rotamer: Outliers : 2.43 % Allowed : 19.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.20), residues: 1587 helix: -2.03 (0.42), residues: 121 sheet: -1.22 (0.24), residues: 446 loop : -1.89 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 238 HIS 0.004 0.001 HIS A 26 PHE 0.024 0.002 PHE A 669 TYR 0.021 0.002 TYR B 557 ARG 0.005 0.001 ARG B 91 *********************** 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 131 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 667 GLU cc_start: 0.5098 (OUTLIER) cc_final: 0.3343 (mm-30) REVERT: A 902 MET cc_start: 0.7055 (pmm) cc_final: 0.5269 (tmm) REVERT: B 344 ILE cc_start: 0.4583 (OUTLIER) cc_final: 0.3986 (mt) outliers start: 32 outliers final: 14 residues processed: 127 average time/residue: 0.2331 time to fit residues: 44.8047 Evaluate side-chains 96 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 587 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 chunk 15 optimal weight: 0.0870 chunk 68 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 152 optimal weight: 20.0000 chunk 75 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 overall best weight: 2.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 665 ASN A 675 ASN ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5886 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 12599 Z= 0.525 Angle : 0.947 10.717 17122 Z= 0.482 Chirality : 0.055 0.380 1922 Planarity : 0.007 0.070 2259 Dihedral : 7.666 62.894 1937 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.80 % Favored : 87.94 % Rotamer: Outliers : 4.34 % Allowed : 18.01 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.20), residues: 1587 helix: -2.26 (0.42), residues: 121 sheet: -1.54 (0.24), residues: 437 loop : -2.08 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 553 HIS 0.010 0.002 HIS A 304 PHE 0.029 0.004 PHE A 87 TYR 0.041 0.003 TYR B 318 ARG 0.012 0.001 ARG A 520 *********************** 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 148 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 90 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.6337 (OUTLIER) cc_final: 0.6114 (mmp80) REVERT: A 427 ILE cc_start: 0.6556 (OUTLIER) cc_final: 0.6141 (tt) REVERT: A 902 MET cc_start: 0.6998 (pmm) cc_final: 0.5247 (tmm) REVERT: B 124 MET cc_start: 0.7552 (mmt) cc_final: 0.7281 (mmt) REVERT: B 207 VAL cc_start: 0.6103 (p) cc_final: 0.5865 (p) REVERT: B 431 PHE cc_start: 0.4764 (m-10) cc_final: 0.4398 (m-10) REVERT: B 557 TYR cc_start: 0.5000 (t80) cc_final: 0.4738 (t80) outliers start: 58 outliers final: 38 residues processed: 142 average time/residue: 0.2233 time to fit residues: 48.1688 Evaluate side-chains 121 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 81 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 156 VAL 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 244 PHE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 178 TYR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 332 VAL 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 127 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 63 optimal weight: 10.0000 chunk 130 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 0 optimal weight: 0.5980 chunk 77 optimal weight: 20.0000 chunk 137 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 665 ASN A 675 ASN A 789 ASN ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5692 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12599 Z= 0.238 Angle : 0.757 11.421 17122 Z= 0.381 Chirality : 0.048 0.387 1922 Planarity : 0.005 0.070 2259 Dihedral : 6.864 62.448 1936 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.57 % Favored : 91.18 % Rotamer: Outliers : 2.65 % Allowed : 20.07 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.20), residues: 1587 helix: -1.80 (0.45), residues: 121 sheet: -1.32 (0.25), residues: 430 loop : -1.87 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 238 HIS 0.005 0.001 HIS A 26 PHE 0.025 0.002 PHE A 87 TYR 0.033 0.002 TYR B 318 ARG 0.004 0.000 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.6243 (OUTLIER) cc_final: 0.5916 (mmp80) REVERT: A 315 GLU cc_start: 0.5390 (mt-10) cc_final: 0.3408 (tt0) REVERT: A 427 ILE cc_start: 0.6211 (OUTLIER) cc_final: 0.5781 (tt) REVERT: A 902 MET cc_start: 0.6934 (pmm) cc_final: 0.5228 (tmm) REVERT: B 120 LEU cc_start: 0.6477 (OUTLIER) cc_final: 0.6271 (mt) outliers start: 35 outliers final: 19 residues processed: 128 average time/residue: 0.2475 time to fit residues: 47.1843 Evaluate side-chains 107 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 178 TYR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 520 TYR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 621 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 0.1980 chunk 137 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 152 optimal weight: 7.9990 chunk 126 optimal weight: 0.8980 chunk 70 optimal weight: 40.0000 chunk 12 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 665 ASN ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5700 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12599 Z= 0.244 Angle : 0.744 10.908 17122 Z= 0.375 Chirality : 0.047 0.334 1922 Planarity : 0.005 0.067 2259 Dihedral : 6.674 69.236 1933 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.33 % Favored : 90.42 % Rotamer: Outliers : 2.65 % Allowed : 21.03 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.20), residues: 1587 helix: -1.66 (0.45), residues: 121 sheet: -1.18 (0.25), residues: 432 loop : -1.78 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 113 HIS 0.004 0.001 HIS A 26 PHE 0.015 0.002 PHE B 56 TYR 0.039 0.002 TYR A 380 ARG 0.004 0.001 ARG A 671 *********************** 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 121 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 86 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.6162 (OUTLIER) cc_final: 0.5833 (mmp80) REVERT: A 427 ILE cc_start: 0.6176 (OUTLIER) cc_final: 0.5714 (tt) REVERT: A 479 LYS cc_start: 0.4066 (tptt) cc_final: 0.3770 (tppt) REVERT: A 703 MET cc_start: 0.3332 (ppp) cc_final: 0.3086 (ppp) REVERT: A 902 MET cc_start: 0.6852 (pmm) cc_final: 0.5283 (tmm) REVERT: B 205 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6216 (mp0) outliers start: 35 outliers final: 24 residues processed: 117 average time/residue: 0.2456 time to fit residues: 43.2975 Evaluate side-chains 105 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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 183 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 285 MET 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 491 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 178 TYR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 287 MET 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 147 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 87 optimal weight: 30.0000 chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 152 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5786 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12599 Z= 0.328 Angle : 0.780 10.400 17122 Z= 0.394 Chirality : 0.049 0.244 1922 Planarity : 0.006 0.068 2259 Dihedral : 6.445 55.422 1929 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.53 % Favored : 89.21 % Rotamer: Outliers : 2.65 % Allowed : 20.37 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.20), residues: 1587 helix: -1.77 (0.44), residues: 122 sheet: -1.16 (0.25), residues: 429 loop : -1.86 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 113 HIS 0.004 0.001 HIS A 26 PHE 0.016 0.002 PHE B 188 TYR 0.032 0.002 TYR B 318 ARG 0.007 0.001 ARG A 671 *********************** 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 114 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 79 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ASP cc_start: 0.5971 (OUTLIER) cc_final: 0.4554 (t0) REVERT: A 208 ARG cc_start: 0.6264 (OUTLIER) cc_final: 0.5934 (mmp80) REVERT: A 427 ILE cc_start: 0.6317 (OUTLIER) cc_final: 0.5562 (tt) REVERT: A 479 LYS cc_start: 0.4282 (tptt) cc_final: 0.3735 (tppt) REVERT: A 902 MET cc_start: 0.6747 (pmm) cc_final: 0.5255 (tmm) outliers start: 35 outliers final: 28 residues processed: 110 average time/residue: 0.2542 time to fit residues: 42.2371 Evaluate side-chains 104 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 73 time to evaluate : 1.481 ------------------------------------------------------------------------------- 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 144 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 285 MET 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 504 LEU Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 178 TYR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 332 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 94 optimal weight: 8.9990 chunk 60 optimal weight: 0.0870 chunk 90 optimal weight: 20.0000 chunk 45 optimal weight: 0.1980 chunk 29 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 138 optimal weight: 20.0000 overall best weight: 0.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5686 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12599 Z= 0.228 Angle : 0.714 9.924 17122 Z= 0.358 Chirality : 0.047 0.289 1922 Planarity : 0.005 0.066 2259 Dihedral : 6.140 56.858 1929 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.31 % Favored : 91.43 % Rotamer: Outliers : 2.50 % Allowed : 20.66 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.20), residues: 1587 helix: -1.51 (0.46), residues: 121 sheet: -1.04 (0.25), residues: 433 loop : -1.78 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 235 HIS 0.004 0.001 HIS A 26 PHE 0.020 0.002 PHE B 431 TYR 0.030 0.002 TYR B 318 ARG 0.006 0.001 ARG A 724 *********************** 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 122 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ASP cc_start: 0.5363 (OUTLIER) cc_final: 0.4021 (t0) REVERT: A 220 SER cc_start: 0.7680 (t) cc_final: 0.7465 (t) REVERT: A 427 ILE cc_start: 0.5964 (OUTLIER) cc_final: 0.5496 (tt) REVERT: A 479 LYS cc_start: 0.4295 (tptt) cc_final: 0.3782 (tppt) REVERT: A 902 MET cc_start: 0.6710 (pmm) cc_final: 0.5246 (tmm) REVERT: B 120 LEU cc_start: 0.6094 (mt) cc_final: 0.5482 (mt) REVERT: B 205 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6230 (mp0) outliers start: 33 outliers final: 25 residues processed: 120 average time/residue: 0.2180 time to fit residues: 40.3299 Evaluate side-chains 105 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 144 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 285 MET 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 661 ARG Chi-restraints excluded: chain B residue 178 TYR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 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 145 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 chunk 141 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 134 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5775 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12599 Z= 0.313 Angle : 0.773 10.011 17122 Z= 0.388 Chirality : 0.048 0.278 1922 Planarity : 0.005 0.051 2259 Dihedral : 6.318 58.032 1929 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.90 % Favored : 89.85 % Rotamer: Outliers : 2.35 % Allowed : 21.25 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.20), residues: 1587 helix: -1.52 (0.46), residues: 121 sheet: -1.07 (0.25), residues: 431 loop : -1.78 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 113 HIS 0.012 0.001 HIS B 509 PHE 0.023 0.002 PHE B 431 TYR 0.030 0.002 TYR B 318 ARG 0.006 0.001 ARG B 216 *********************** 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 110 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 79 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ASP cc_start: 0.5897 (OUTLIER) cc_final: 0.4543 (t0) REVERT: A 208 ARG cc_start: 0.6227 (OUTLIER) cc_final: 0.5889 (mmp80) REVERT: A 315 GLU cc_start: 0.5344 (mt-10) cc_final: 0.3371 (tt0) REVERT: A 427 ILE cc_start: 0.6169 (OUTLIER) cc_final: 0.5758 (tt) REVERT: A 479 LYS cc_start: 0.4212 (tptt) cc_final: 0.3512 (mmtm) REVERT: A 902 MET cc_start: 0.6727 (pmm) cc_final: 0.5331 (tmm) REVERT: B 205 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6198 (mp0) outliers start: 31 outliers final: 25 residues processed: 108 average time/residue: 0.2494 time to fit residues: 40.2629 Evaluate side-chains 104 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 1.477 ------------------------------------------------------------------------------- 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 144 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 307 LEU 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 B residue 178 TYR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 621 ASP Chi-restraints excluded: chain B residue 653 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 0.6980 chunk 71 optimal weight: 0.0060 chunk 104 optimal weight: 0.0980 chunk 157 optimal weight: 0.2980 chunk 144 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN ** A 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5643 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12599 Z= 0.201 Angle : 0.704 9.665 17122 Z= 0.349 Chirality : 0.046 0.260 1922 Planarity : 0.005 0.051 2259 Dihedral : 5.963 59.159 1929 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.93 % Favored : 91.81 % Rotamer: Outliers : 1.84 % Allowed : 21.69 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.21), residues: 1587 helix: -1.37 (0.47), residues: 122 sheet: -0.99 (0.25), residues: 437 loop : -1.68 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 235 HIS 0.014 0.001 HIS B 509 PHE 0.013 0.002 PHE B 421 TYR 0.048 0.002 TYR B 557 ARG 0.005 0.000 ARG A 147 ********************** 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 104 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 SER cc_start: 0.7642 (t) cc_final: 0.7422 (t) REVERT: A 315 GLU cc_start: 0.5281 (mt-10) cc_final: 0.3365 (tt0) REVERT: A 479 LYS cc_start: 0.4209 (tptt) cc_final: 0.3487 (mmtm) REVERT: A 902 MET cc_start: 0.6700 (pmm) cc_final: 0.5378 (tmm) REVERT: B 205 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6269 (mp0) outliers start: 24 outliers final: 18 residues processed: 103 average time/residue: 0.2606 time to fit residues: 39.8977 Evaluate side-chains 92 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain B residue 178 TYR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 621 ASP Chi-restraints excluded: chain B residue 653 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 0.0050 chunk 125 optimal weight: 0.5980 chunk 52 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 7 optimal weight: 0.0040 overall best weight: 0.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.231516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.195893 restraints weight = 53328.556| |-----------------------------------------------------------------------------| r_work (start): 0.4571 rms_B_bonded: 4.45 r_work (final): 0.4571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4571 r_free = 0.4571 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 = 0.4568 r_free = 0.4568 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| r_final: 0.4568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5593 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12599 Z= 0.201 Angle : 0.689 9.557 17122 Z= 0.342 Chirality : 0.045 0.259 1922 Planarity : 0.005 0.053 2259 Dihedral : 5.820 59.902 1929 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.19 % Favored : 91.56 % Rotamer: Outliers : 1.69 % Allowed : 21.76 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.21), residues: 1587 helix: -1.34 (0.47), residues: 122 sheet: -0.97 (0.25), residues: 447 loop : -1.67 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 113 HIS 0.011 0.001 HIS B 509 PHE 0.013 0.001 PHE B 431 TYR 0.032 0.001 TYR B 557 ARG 0.008 0.001 ARG B 489 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2522.60 seconds wall clock time: 46 minutes 58.09 seconds (2818.09 seconds total)