Starting phenix.real_space_refine on Wed Feb 4 20:47:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e8a_47713/02_2026/9e8a_47713.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e8a_47713/02_2026/9e8a_47713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e8a_47713/02_2026/9e8a_47713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e8a_47713/02_2026/9e8a_47713.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e8a_47713/02_2026/9e8a_47713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e8a_47713/02_2026/9e8a_47713.map" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.025 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: 7 Type Number sf(0) Gaussians Ca 7 9.91 5 Mg 1 5.21 5 S 99 5.16 5 C 7822 2.51 5 N 2139 2.21 5 O 2499 1.98 5 H 22 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12589 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7002 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 915, 6994 Classifications: {'peptide': 915} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 853} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 915, 6994 Classifications: {'peptide': 915} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 853} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 7151 Chain: "B" Number of atoms: 5234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5234 Classifications: {'peptide': 683} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 649} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "D" 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: "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: "F" 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: "G" 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: "H" 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: "I" 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: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 47 Unusual residues: {' CA': 5, 'NAG': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 2, ' MG': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.56, per 1000 atoms: 0.36 Number of scatterers: 12589 At special positions: 0 Unit cell: (96.3, 129.47, 135.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 7 19.99 S 99 16.00 Mg 1 11.99 O 2499 8.00 N 2139 7.00 C 7822 6.00 H 22 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 515 " distance=2.03 Simple disulfide: pdb=" SG CYS A 521 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 639 " distance=2.03 Simple disulfide: pdb=" SG CYS A 705 " - pdb=" SG CYS A 718 " distance=2.03 Simple disulfide: pdb=" SG CYS A 857 " - pdb=" SG CYS A 921 " distance=2.03 Simple disulfide: pdb=" SG CYS A 911 " - pdb=" SG CYS A 916 " distance=2.03 Simple disulfide: pdb=" SG CYS B 31 " - pdb=" SG CYS B 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 39 " - pdb=" SG CYS B 461 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 64 " distance=2.02 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 210 " distance=2.03 Simple disulfide: pdb=" SG CYS B 258 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 400 " - pdb=" SG CYS B 412 " distance=2.04 Simple disulfide: pdb=" SG CYS B 432 " - pdb=" SG CYS B 459 " distance=2.03 Simple disulfide: pdb=" SG CYS B 463 " - pdb=" SG CYS B 483 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 488 " - pdb=" SG CYS B 497 " distance=2.03 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 529 " distance=2.03 Simple disulfide: pdb=" SG CYS B 512 " - pdb=" SG CYS B 527 " distance=2.03 Simple disulfide: pdb=" SG CYS B 521 " - pdb=" SG CYS B 532 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 547 " distance=2.03 Simple disulfide: pdb=" SG CYS B 549 " - pdb=" SG CYS B 570 " distance=2.03 Simple disulfide: pdb=" SG CYS B 554 " - pdb=" SG CYS B 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 562 " - pdb=" SG CYS B 573 " distance=2.04 Simple disulfide: pdb=" SG CYS B 575 " - pdb=" SG CYS B 584 " distance=2.03 Simple disulfide: pdb=" SG CYS B 586 " - pdb=" SG CYS B 609 " distance=2.03 Simple disulfide: pdb=" SG CYS B 593 " - pdb=" SG CYS B 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 593 " - pdb=" SG CYS B 607 " distance=2.03 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 612 " distance=2.02 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 624 " distance=2.03 Simple disulfide: pdb=" SG CYS B 627 " - pdb=" SG CYS B 630 " distance=2.03 Simple disulfide: pdb=" SG CYS B 634 " - pdb=" SG CYS B 681 " distance=2.03 Simple disulfide: pdb=" SG CYS B 643 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 689 " - pdb=" SG CYS B 713 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " BMA J 2 " - " NAG J 3 " " NAG J 3 " - " NAG J 4 " BETA1-6 " BMA J 1 " - " BMA J 2 " NAG-ASN " NAG A1105 " - " ASN A 280 " " NAG A1108 " - " ASN A 711 " " NAG B 804 " - " ASN B 680 " " NAG E 1 " - " ASN B 125 " " NAG F 1 " - " ASN B 585 " " NAG G 1 " - " ASN A 962 " " NAG H 1 " - " ASN B 397 " " NAG I 1 " - " ASN B 346 " Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 1.0 seconds 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2934 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 27 sheets defined 14.4% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 182 through 189 removed outlier: 3.662A pdb=" N TYR A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 231 through 238 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.804A pdb=" N LYS A 502 " --> pdb=" O PRO A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 609 removed outlier: 4.061A pdb=" N GLU A 608 " --> pdb=" O PRO A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 744 removed outlier: 3.600A pdb=" N GLU A 743 " --> pdb=" O ASN A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 947 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 38 through 44 removed outlier: 3.787A pdb=" N ALA B 44 " --> pdb=" O GLN B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 150 through 157 removed outlier: 3.531A pdb=" N TRP B 155 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 156 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 169 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 201 through 207 removed outlier: 4.370A pdb=" N ASP B 205 " --> pdb=" O PRO B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 235 removed outlier: 4.073A pdb=" N PHE B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN B 230 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 258 removed outlier: 3.541A pdb=" N ALA B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 284 through 288 removed outlier: 3.777A pdb=" N ARG B 287 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 311 removed outlier: 4.494A pdb=" N THR B 311 " --> pdb=" O SER B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 329 Processing helix chain 'B' and resid 340 through 351 removed outlier: 3.562A pdb=" N LEU B 350 " --> pdb=" O ASN B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 378 Processing helix chain 'B' and resid 461 through 465 Processing helix chain 'B' and resid 519 through 523 Processing helix chain 'B' and resid 560 through 564 Processing helix chain 'B' and resid 599 through 604 Processing helix chain 'B' and resid 632 through 645 removed outlier: 3.777A pdb=" N PHE B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLU B 639 " --> pdb=" O THR B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 660 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 43 removed outlier: 6.236A pdb=" N ASP A 465 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 455 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER A 451 " --> pdb=" O GLY A 469 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 58 removed outlier: 4.446A pdb=" N VAL A 84 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 110 Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 131 Processing sheet with id=AA5, first strand: chain 'A' and resid 203 through 206 removed outlier: 3.587A pdb=" N SER A 203 " --> pdb=" O GLY A 215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 270 through 273 removed outlier: 6.489A pdb=" N VAL A 298 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ARG A 310 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE A 300 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 327 removed outlier: 3.535A pdb=" N LEU A 376 " --> pdb=" O LEU A 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 345 through 347 Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 395 removed outlier: 6.276A pdb=" N ILE A 391 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ALA A 408 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ALA A 406 " --> pdb=" O PRO A 393 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A 395 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN A 436 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 425 through 426 Processing sheet with id=AB2, first strand: chain 'A' and resid 552 through 554 removed outlier: 4.332A pdb=" N SER A 514 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL A 485 " --> pdb=" O HIS A 618 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ASP A 620 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ALA A 487 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 496 through 497 Processing sheet with id=AB4, first strand: chain 'A' and resid 643 through 650 removed outlier: 3.596A pdb=" N MET A 734 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA A 728 " --> pdb=" O ASN A 670 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLY A 731 " --> pdb=" O SER A 695 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N SER A 695 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA A 733 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ALA A 693 " --> pdb=" O ALA A 733 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU A 735 " --> pdb=" O MET A 691 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.116A pdb=" N LEU A 654 " --> pdb=" O ARG A 774 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 751 " --> pdb=" O HIS A 683 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG A 714 " --> pdb=" O LEU A 684 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 675 through 676 Processing sheet with id=AB7, first strand: chain 'A' and resid 780 through 786 removed outlier: 6.525A pdb=" N MET A 933 " --> pdb=" O PRO A 851 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR A 935 " --> pdb=" O ILE A 849 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ILE A 849 " --> pdb=" O THR A 935 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU A 937 " --> pdb=" O LEU A 847 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 907 through 909 removed outlier: 6.414A pdb=" N VAL A 907 " --> pdb=" O VAL A 954 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN A 956 " --> pdb=" O VAL A 907 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL A 909 " --> pdb=" O GLN A 956 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N HIS A 958 " --> pdb=" O VAL A 909 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLN A 924 " --> pdb=" O GLY A 827 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N HIS A 829 " --> pdb=" O ASP A 922 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP A 922 " --> pdb=" O HIS A 829 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER A 831 " --> pdb=" O GLN A 920 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N GLN A 920 " --> pdb=" O SER A 831 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N HIS A 833 " --> pdb=" O VAL A 918 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL A 918 " --> pdb=" O HIS A 833 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 907 through 909 removed outlier: 6.414A pdb=" N VAL A 907 " --> pdb=" O VAL A 954 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN A 956 " --> pdb=" O VAL A 907 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL A 909 " --> pdb=" O GLN A 956 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N HIS A 958 " --> pdb=" O VAL A 909 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 86 through 91 removed outlier: 6.746A pdb=" N ARG B 113 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE B 114 " --> pdb=" O GLN B 454 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N THR B 456 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 116 " --> pdb=" O THR B 456 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AC3, first strand: chain 'B' and resid 216 through 223 removed outlier: 6.514A pdb=" N PHE B 179 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N THR B 221 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ILE B 177 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR B 223 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU B 175 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N HIS B 270 " --> pdb=" O ASN B 331 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE B 333 " --> pdb=" O HIS B 270 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU B 272 " --> pdb=" O ILE B 333 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA B 335 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE B 274 " --> pdb=" O ALA B 335 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 467 through 468 Processing sheet with id=AC5, first strand: chain 'B' and resid 525 through 527 Processing sheet with id=AC6, first strand: chain 'B' and resid 566 through 569 Processing sheet with id=AC7, first strand: chain 'B' and resid 579 through 580 Processing sheet with id=AC8, first strand: chain 'B' and resid 606 through 608 Processing sheet with id=AC9, first strand: chain 'B' and resid 679 through 684 397 hydrogen bonds defined for protein. 1004 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: 2.72 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.87 - 1.06: 22 1.06 - 1.25: 2081 1.25 - 1.44: 3374 1.44 - 1.63: 7240 1.63 - 1.82: 124 Bond restraints: 12841 Sorted by residual: bond pdb=" N ARG A 948 " pdb=" CA ARG A 948 " ideal model delta sigma weight residual 1.458 1.487 -0.029 7.40e-03 1.83e+04 1.57e+01 bond pdb=" N VAL A 602 " pdb=" CA VAL A 602 " ideal model delta sigma weight residual 1.459 1.508 -0.049 1.25e-02 6.40e+03 1.52e+01 bond pdb=" N VAL A 825 " pdb=" CA VAL A 825 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.14e-02 7.69e+03 1.05e+01 bond pdb=" N VAL A 963 " pdb=" CA VAL A 963 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.19e-02 7.06e+03 1.05e+01 bond pdb=" N GLY A 978 " pdb=" CA GLY A 978 " ideal model delta sigma weight residual 1.444 1.476 -0.033 1.02e-02 9.61e+03 1.02e+01 ... (remaining 12836 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 16755 1.95 - 3.89: 657 3.89 - 5.84: 51 5.84 - 7.78: 1 7.78 - 9.73: 1 Bond angle restraints: 17465 Sorted by residual: angle pdb=" C CYS B 593 " pdb=" CA CYS B 593 " pdb=" CB CYS B 593 " ideal model delta sigma weight residual 110.88 101.15 9.73 1.57e+00 4.06e-01 3.84e+01 angle pdb=" CA GLY B 581 " pdb=" C GLY B 581 " pdb=" O GLY B 581 " ideal model delta sigma weight residual 122.22 118.31 3.91 6.50e-01 2.37e+00 3.62e+01 angle pdb=" C ASN B 74 " pdb=" CA ASN B 74 " pdb=" CB ASN B 74 " ideal model delta sigma weight residual 116.63 110.84 5.79 1.16e+00 7.43e-01 2.49e+01 angle pdb=" CA GLY C 494 " pdb=" C GLY C 494 " pdb=" O GLY C 494 " ideal model delta sigma weight residual 122.24 117.75 4.49 1.08e+00 8.57e-01 1.73e+01 angle pdb=" C CYS B 601 " pdb=" CA CYS B 601 " pdb=" CB CYS B 601 " ideal model delta sigma weight residual 111.80 117.86 -6.06 1.46e+00 4.69e-01 1.72e+01 ... (remaining 17460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.24: 7813 23.24 - 46.48: 208 46.48 - 69.72: 46 69.72 - 92.96: 18 92.96 - 116.21: 33 Dihedral angle restraints: 8118 sinusoidal: 3534 harmonic: 4584 Sorted by residual: dihedral pdb=" CD ARG A 977 " pdb=" NE ARG A 977 " pdb=" CZ ARG A 977 " pdb=" NH1 ARG A 977 " ideal model delta sinusoidal sigma weight residual 0.00 47.81 -47.81 1 1.00e+01 1.00e-02 3.15e+01 dihedral pdb=" CB CYS B 627 " pdb=" SG CYS B 627 " pdb=" SG CYS B 630 " pdb=" CB CYS B 630 " ideal model delta sinusoidal sigma weight residual -86.00 -133.56 47.56 1 1.00e+01 1.00e-02 3.12e+01 dihedral pdb=" CB CYS B 203 " pdb=" SG CYS B 203 " pdb=" SG CYS B 210 " pdb=" CB CYS B 210 " ideal model delta sinusoidal sigma weight residual -86.00 -125.57 39.57 1 1.00e+01 1.00e-02 2.20e+01 ... (remaining 8115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.253: 1977 0.253 - 0.506: 6 0.506 - 0.759: 1 0.759 - 1.012: 0 1.012 - 1.265: 1 Chirality restraints: 1985 Sorted by residual: chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.13 -1.27 2.00e-02 2.50e+03 4.00e+03 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-02 2.50e+03 3.69e+02 chirality pdb=" C1 NAG J 4 " pdb=" O4 NAG J 3 " pdb=" C2 NAG J 4 " pdb=" O5 NAG J 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-02 2.50e+03 2.84e+02 ... (remaining 1982 not shown) Planarity restraints: 2291 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " -0.323 2.00e-02 2.50e+03 2.79e-01 9.75e+02 pdb=" C7 NAG G 1 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " -0.142 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " 0.498 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.297 2.00e-02 2.50e+03 2.55e-01 8.13e+02 pdb=" C7 NAG E 2 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.164 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.449 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " -0.272 2.00e-02 2.50e+03 2.33e-01 6.79e+02 pdb=" C7 NAG E 1 " 0.064 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.162 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " 0.407 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " -0.038 2.00e-02 2.50e+03 ... (remaining 2288 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.53: 182 2.53 - 3.05: 9013 3.05 - 3.57: 14712 3.57 - 4.08: 23396 4.08 - 4.60: 32826 Nonbonded interactions: 80129 Sorted by model distance: nonbonded pdb=" OD2 ASP B 152 " pdb="CA CA B 803 " model vdw 2.018 2.390 nonbonded pdb=" OD1 ASP B 152 " pdb="CA CA B 803 " model vdw 2.037 2.390 nonbonded pdb=" OD1 ASN B 241 " pdb="CA CA B 802 " model vdw 2.201 2.390 nonbonded pdb=" O ASP B 647 " pdb=" NH1 ARG B 648 " model vdw 2.205 2.950 nonbonded pdb=" OD1 ASP A 459 " pdb="CA CA A1104 " model vdw 2.206 2.390 ... (remaining 80124 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 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.970 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: 0.140 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.450 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.050 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:7.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12875 Z= 0.390 Angle : 0.797 15.756 17546 Z= 0.483 Chirality : 0.064 1.265 1985 Planarity : 0.016 0.367 2280 Dihedral : 13.992 116.205 5067 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 25.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.16 % Favored : 94.65 % Rotamer: Outliers : 2.57 % Allowed : 5.06 % Favored : 92.37 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.22), residues: 1591 helix: 0.09 (0.46), residues: 144 sheet: 0.42 (0.23), residues: 534 loop : -0.72 (0.22), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 948 TYR 0.011 0.001 TYR B 695 PHE 0.012 0.001 PHE B 396 TRP 0.009 0.001 TRP A 266 HIS 0.002 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00578 (12819) covalent geometry : angle 0.74252 (17415) SS BOND : bond 0.00306 ( 37) SS BOND : angle 1.02207 ( 74) hydrogen bonds : bond 0.24346 ( 397) hydrogen bonds : angle 10.02427 ( 1004) link_BETA1-4 : bond 0.03900 ( 10) link_BETA1-4 : angle 5.79219 ( 30) link_BETA1-6 : bond 0.03580 ( 1) link_BETA1-6 : angle 4.65135 ( 3) link_NAG-ASN : bond 0.00767 ( 8) link_NAG-ASN : angle 4.04535 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 THR cc_start: 0.9392 (p) cc_final: 0.9147 (p) REVERT: A 433 ARG cc_start: 0.8819 (mmm-85) cc_final: 0.8471 (tpp80) REVERT: A 532 LYS cc_start: 0.9181 (tptt) cc_final: 0.8871 (tppt) REVERT: A 547 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8191 (tmm160) REVERT: A 659 ASP cc_start: 0.8702 (p0) cc_final: 0.8353 (p0) REVERT: A 706 ASN cc_start: 0.8550 (m-40) cc_final: 0.8331 (m-40) REVERT: A 719 GLU cc_start: 0.8074 (mp0) cc_final: 0.7591 (mp0) REVERT: A 760 GLN cc_start: 0.8755 (mp10) cc_final: 0.8352 (mp10) REVERT: A 786 PHE cc_start: 0.8491 (m-80) cc_final: 0.8280 (m-10) REVERT: A 815 TYR cc_start: 0.8188 (m-80) cc_final: 0.7448 (m-10) REVERT: A 948 ARG cc_start: 0.7505 (ttm110) cc_final: 0.7024 (ttp-110) REVERT: A 950 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7242 (mm) REVERT: A 961 PHE cc_start: 0.8207 (t80) cc_final: 0.7863 (t80) REVERT: A 981 GLN cc_start: 0.8712 (mt0) cc_final: 0.8007 (mm110) REVERT: A 983 TRP cc_start: 0.7457 (p90) cc_final: 0.7161 (p90) REVERT: B 41 GLN cc_start: 0.8421 (tt0) cc_final: 0.7977 (tt0) REVERT: B 158 GLN cc_start: 0.8564 (tp40) cc_final: 0.8340 (tp40) REVERT: B 267 ASP cc_start: 0.8531 (p0) cc_final: 0.8216 (p0) REVERT: B 382 GLU cc_start: 0.8568 (tt0) cc_final: 0.8325 (tt0) REVERT: B 542 ILE cc_start: 0.9126 (mt) cc_final: 0.8888 (mp) REVERT: B 582 TYR cc_start: 0.7553 (t80) cc_final: 0.7316 (t80) REVERT: B 645 LYS cc_start: 0.8078 (tmtt) cc_final: 0.7622 (tmmm) outliers start: 35 outliers final: 13 residues processed: 173 average time/residue: 0.6783 time to fit residues: 126.7052 Evaluate side-chains 123 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 461 CYS Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 630 CYS Chi-restraints excluded: chain B residue 673 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 78 GLN A 95 GLN A 482 GLN A 490 GLN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 ASN A 622 HIS A 642 GLN A 644 GLN A 819 ASN ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 HIS A 837 GLN ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 930 GLN ** A 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 GLN A 981 GLN B 69 ASN B 167 GLN B 300 HIS B 339 ASN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 GLN ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.112954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.068131 restraints weight = 24545.693| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.87 r_work: 0.2788 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12875 Z= 0.134 Angle : 0.589 10.525 17546 Z= 0.286 Chirality : 0.044 0.300 1985 Planarity : 0.004 0.060 2280 Dihedral : 13.051 108.596 2205 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 30.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.72 % Favored : 95.22 % Rotamer: Outliers : 1.98 % Allowed : 9.98 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.22), residues: 1591 helix: -0.09 (0.44), residues: 156 sheet: 0.36 (0.23), residues: 536 loop : -0.63 (0.22), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 121 TYR 0.013 0.001 TYR A 946 PHE 0.008 0.001 PHE A 101 TRP 0.009 0.001 TRP A 266 HIS 0.002 0.001 HIS B 281 Details of bonding type rmsd covalent geometry : bond 0.00300 (12819) covalent geometry : angle 0.56167 (17415) SS BOND : bond 0.00374 ( 37) SS BOND : angle 1.29507 ( 74) hydrogen bonds : bond 0.04000 ( 397) hydrogen bonds : angle 7.21509 ( 1004) link_BETA1-4 : bond 0.00483 ( 10) link_BETA1-4 : angle 2.16914 ( 30) link_BETA1-6 : bond 0.00331 ( 1) link_BETA1-6 : angle 3.51741 ( 3) link_NAG-ASN : bond 0.00343 ( 8) link_NAG-ASN : angle 3.48689 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 THR cc_start: 0.9388 (p) cc_final: 0.9130 (p) REVERT: A 433 ARG cc_start: 0.9156 (mmm-85) cc_final: 0.8865 (tpp80) REVERT: A 532 LYS cc_start: 0.9289 (tptt) cc_final: 0.8912 (tppt) REVERT: A 659 ASP cc_start: 0.8791 (p0) cc_final: 0.8455 (p0) REVERT: A 706 ASN cc_start: 0.8757 (m-40) cc_final: 0.8496 (m-40) REVERT: A 719 GLU cc_start: 0.8295 (mp0) cc_final: 0.7749 (mp0) REVERT: A 760 GLN cc_start: 0.8801 (mp10) cc_final: 0.8478 (mp10) REVERT: A 815 TYR cc_start: 0.7412 (m-80) cc_final: 0.6524 (m-10) REVERT: A 948 ARG cc_start: 0.7583 (ttm110) cc_final: 0.7081 (ttp80) REVERT: A 960 TRP cc_start: 0.7188 (t60) cc_final: 0.6877 (t60) REVERT: A 961 PHE cc_start: 0.8536 (t80) cc_final: 0.8085 (t80) REVERT: A 983 TRP cc_start: 0.7827 (p90) cc_final: 0.7599 (p90) REVERT: B 41 GLN cc_start: 0.8983 (tt0) cc_final: 0.8450 (tt0) REVERT: B 382 GLU cc_start: 0.8789 (tt0) cc_final: 0.8564 (tt0) REVERT: B 542 ILE cc_start: 0.9115 (mt) cc_final: 0.8895 (mp) REVERT: B 582 TYR cc_start: 0.7701 (t80) cc_final: 0.7424 (t80) REVERT: B 632 ASP cc_start: 0.8063 (t0) cc_final: 0.7770 (t0) REVERT: B 710 GLU cc_start: 0.8517 (pm20) cc_final: 0.7708 (tp30) REVERT: C 493 ARG cc_start: 0.6488 (OUTLIER) cc_final: 0.5671 (ttp-170) outliers start: 27 outliers final: 15 residues processed: 138 average time/residue: 0.6060 time to fit residues: 91.4654 Evaluate side-chains 115 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 461 CYS Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 630 CYS Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain C residue 493 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 37 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 GLN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 GLN ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 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 = 0.3628 r_free = 0.3628 target = 0.110514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.064609 restraints weight = 32584.523| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.27 r_work: 0.2717 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 12875 Z= 0.273 Angle : 0.628 9.182 17546 Z= 0.307 Chirality : 0.046 0.338 1985 Planarity : 0.004 0.054 2280 Dihedral : 11.321 102.672 2199 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 31.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.23 % Favored : 93.71 % Rotamer: Outliers : 2.86 % Allowed : 10.05 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.21), residues: 1591 helix: -0.33 (0.42), residues: 156 sheet: 0.16 (0.22), residues: 536 loop : -0.80 (0.22), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 473 TYR 0.024 0.002 TYR A 690 PHE 0.015 0.002 PHE B 447 TRP 0.012 0.001 TRP B 264 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00624 (12819) covalent geometry : angle 0.60688 (17415) SS BOND : bond 0.00363 ( 37) SS BOND : angle 1.31833 ( 74) hydrogen bonds : bond 0.03938 ( 397) hydrogen bonds : angle 6.64140 ( 1004) link_BETA1-4 : bond 0.00399 ( 10) link_BETA1-4 : angle 1.96195 ( 30) link_BETA1-6 : bond 0.00380 ( 1) link_BETA1-6 : angle 3.43577 ( 3) link_NAG-ASN : bond 0.00463 ( 8) link_NAG-ASN : angle 3.02516 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 102 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ARG cc_start: 0.9028 (mmm-85) cc_final: 0.8720 (tpp80) REVERT: A 532 LYS cc_start: 0.9233 (tptt) cc_final: 0.8843 (tppt) REVERT: A 659 ASP cc_start: 0.8799 (p0) cc_final: 0.8452 (p0) REVERT: A 706 ASN cc_start: 0.8632 (m-40) cc_final: 0.8360 (m-40) REVERT: A 719 GLU cc_start: 0.8154 (mp0) cc_final: 0.7484 (mp0) REVERT: A 760 GLN cc_start: 0.8893 (mp10) cc_final: 0.8574 (mp10) REVERT: A 815 TYR cc_start: 0.7283 (m-80) cc_final: 0.6486 (m-10) REVERT: A 828 LEU cc_start: 0.8864 (tm) cc_final: 0.8622 (tm) REVERT: A 926 MET cc_start: 0.7308 (tpt) cc_final: 0.6993 (tpt) REVERT: A 939 PHE cc_start: 0.5917 (OUTLIER) cc_final: 0.5350 (m-80) REVERT: A 960 TRP cc_start: 0.7357 (t60) cc_final: 0.7156 (t60) REVERT: A 961 PHE cc_start: 0.8536 (t80) cc_final: 0.8070 (t80) REVERT: B 41 GLN cc_start: 0.8829 (tt0) cc_final: 0.8215 (tt0) REVERT: B 632 ASP cc_start: 0.8154 (t0) cc_final: 0.7870 (t0) REVERT: B 664 GLU cc_start: 0.5357 (OUTLIER) cc_final: 0.4746 (mp0) outliers start: 39 outliers final: 22 residues processed: 127 average time/residue: 0.6066 time to fit residues: 84.1652 Evaluate side-chains 118 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 630 CYS Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 683 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 130 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 120 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 92 optimal weight: 0.8980 chunk 158 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 55 optimal weight: 0.0980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.112106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.066856 restraints weight = 22234.827| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.68 r_work: 0.2751 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12875 Z= 0.132 Angle : 0.540 9.108 17546 Z= 0.259 Chirality : 0.044 0.323 1985 Planarity : 0.003 0.054 2280 Dihedral : 10.234 103.701 2198 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 31.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.03 % Favored : 94.84 % Rotamer: Outliers : 1.98 % Allowed : 11.30 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.21), residues: 1591 helix: -0.14 (0.42), residues: 155 sheet: 0.32 (0.23), residues: 508 loop : -0.78 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 473 TYR 0.014 0.001 TYR A 946 PHE 0.008 0.001 PHE A 750 TRP 0.011 0.001 TRP A 266 HIS 0.002 0.000 HIS B 281 Details of bonding type rmsd covalent geometry : bond 0.00295 (12819) covalent geometry : angle 0.51883 (17415) SS BOND : bond 0.00266 ( 37) SS BOND : angle 1.21022 ( 74) hydrogen bonds : bond 0.02976 ( 397) hydrogen bonds : angle 6.25526 ( 1004) link_BETA1-4 : bond 0.00377 ( 10) link_BETA1-4 : angle 1.87605 ( 30) link_BETA1-6 : bond 0.00498 ( 1) link_BETA1-6 : angle 3.30173 ( 3) link_NAG-ASN : bond 0.00235 ( 8) link_NAG-ASN : angle 2.79477 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 THR cc_start: 0.9296 (p) cc_final: 0.9077 (p) REVERT: A 433 ARG cc_start: 0.9162 (mmm-85) cc_final: 0.8897 (tpp80) REVERT: A 532 LYS cc_start: 0.9288 (tptt) cc_final: 0.8927 (tppt) REVERT: A 659 ASP cc_start: 0.8792 (p0) cc_final: 0.8440 (p0) REVERT: A 706 ASN cc_start: 0.8748 (m-40) cc_final: 0.8485 (m-40) REVERT: A 719 GLU cc_start: 0.8470 (mp0) cc_final: 0.7811 (mp0) REVERT: A 760 GLN cc_start: 0.8997 (mp10) cc_final: 0.8573 (mp10) REVERT: A 815 TYR cc_start: 0.7280 (m-80) cc_final: 0.6394 (m-10) REVERT: A 828 LEU cc_start: 0.8955 (tm) cc_final: 0.8644 (tm) REVERT: A 926 MET cc_start: 0.7404 (tpt) cc_final: 0.7138 (tpt) REVERT: A 939 PHE cc_start: 0.6165 (OUTLIER) cc_final: 0.5444 (m-80) REVERT: A 961 PHE cc_start: 0.8513 (t80) cc_final: 0.8052 (t80) REVERT: B 41 GLN cc_start: 0.8994 (tt0) cc_final: 0.8417 (tt0) REVERT: B 57 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6441 (tm) REVERT: B 253 MET cc_start: 0.9386 (OUTLIER) cc_final: 0.9039 (tpp) REVERT: B 632 ASP cc_start: 0.8270 (t0) cc_final: 0.7960 (t0) REVERT: B 664 GLU cc_start: 0.5748 (OUTLIER) cc_final: 0.4837 (mp0) outliers start: 27 outliers final: 17 residues processed: 113 average time/residue: 0.6302 time to fit residues: 77.8698 Evaluate side-chains 114 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 630 CYS Chi-restraints excluded: chain B residue 646 PHE Chi-restraints excluded: chain B residue 664 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 106 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 155 optimal weight: 30.0000 chunk 97 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 142 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.110042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.065274 restraints weight = 22276.164| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.72 r_work: 0.2751 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12875 Z= 0.264 Angle : 0.611 9.790 17546 Z= 0.296 Chirality : 0.045 0.329 1985 Planarity : 0.004 0.051 2280 Dihedral : 9.263 101.480 2197 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 32.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.60 % Favored : 93.27 % Rotamer: Outliers : 2.35 % Allowed : 11.37 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.21), residues: 1591 helix: -0.24 (0.42), residues: 149 sheet: 0.03 (0.22), residues: 535 loop : -0.85 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 473 TYR 0.021 0.002 TYR A 690 PHE 0.013 0.002 PHE B 447 TRP 0.012 0.001 TRP B 264 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00609 (12819) covalent geometry : angle 0.59062 (17415) SS BOND : bond 0.00313 ( 37) SS BOND : angle 1.29319 ( 74) hydrogen bonds : bond 0.03355 ( 397) hydrogen bonds : angle 6.25525 ( 1004) link_BETA1-4 : bond 0.00422 ( 10) link_BETA1-4 : angle 2.01888 ( 30) link_BETA1-6 : bond 0.00609 ( 1) link_BETA1-6 : angle 3.03828 ( 3) link_NAG-ASN : bond 0.00421 ( 8) link_NAG-ASN : angle 2.85259 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 THR cc_start: 0.9371 (p) cc_final: 0.9156 (p) REVERT: A 433 ARG cc_start: 0.9110 (mmm-85) cc_final: 0.8803 (tpp80) REVERT: A 532 LYS cc_start: 0.9256 (tptt) cc_final: 0.8850 (tppt) REVERT: A 659 ASP cc_start: 0.8823 (p0) cc_final: 0.8473 (p0) REVERT: A 706 ASN cc_start: 0.8633 (m-40) cc_final: 0.8371 (m-40) REVERT: A 719 GLU cc_start: 0.8364 (mp0) cc_final: 0.7653 (mp0) REVERT: A 760 GLN cc_start: 0.8897 (mp10) cc_final: 0.8477 (mp10) REVERT: A 815 TYR cc_start: 0.7263 (m-80) cc_final: 0.6414 (m-10) REVERT: A 828 LEU cc_start: 0.8945 (tm) cc_final: 0.8647 (tm) REVERT: A 926 MET cc_start: 0.7324 (tpt) cc_final: 0.6991 (tpt) REVERT: A 939 PHE cc_start: 0.6069 (OUTLIER) cc_final: 0.5411 (m-80) REVERT: A 961 PHE cc_start: 0.8543 (t80) cc_final: 0.8084 (t80) REVERT: B 41 GLN cc_start: 0.8887 (tt0) cc_final: 0.8255 (tt0) REVERT: B 57 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6357 (tm) REVERT: B 253 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.8883 (tpp) REVERT: B 632 ASP cc_start: 0.8256 (t0) cc_final: 0.7970 (t0) REVERT: B 664 GLU cc_start: 0.5639 (OUTLIER) cc_final: 0.5310 (tm-30) outliers start: 32 outliers final: 23 residues processed: 120 average time/residue: 0.6454 time to fit residues: 84.7630 Evaluate side-chains 126 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 630 CYS Chi-restraints excluded: chain B residue 646 PHE Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain C residue 493 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 4 optimal weight: 0.2980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.111312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.066002 restraints weight = 25619.791| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.94 r_work: 0.2757 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12875 Z= 0.152 Angle : 0.545 9.345 17546 Z= 0.262 Chirality : 0.043 0.298 1985 Planarity : 0.003 0.051 2280 Dihedral : 8.725 102.687 2197 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 32.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.53 % Favored : 94.34 % Rotamer: Outliers : 2.13 % Allowed : 11.89 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.21), residues: 1591 helix: -0.17 (0.42), residues: 155 sheet: 0.09 (0.23), residues: 518 loop : -0.79 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 473 TYR 0.019 0.001 TYR B 683 PHE 0.012 0.001 PHE B 693 TRP 0.011 0.001 TRP A 266 HIS 0.002 0.000 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00348 (12819) covalent geometry : angle 0.52208 (17415) SS BOND : bond 0.00243 ( 37) SS BOND : angle 1.27464 ( 74) hydrogen bonds : bond 0.02940 ( 397) hydrogen bonds : angle 6.03887 ( 1004) link_BETA1-4 : bond 0.00404 ( 10) link_BETA1-4 : angle 2.09156 ( 30) link_BETA1-6 : bond 0.00624 ( 1) link_BETA1-6 : angle 3.24246 ( 3) link_NAG-ASN : bond 0.00248 ( 8) link_NAG-ASN : angle 2.71209 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 THR cc_start: 0.9332 (p) cc_final: 0.9105 (p) REVERT: A 433 ARG cc_start: 0.9110 (mmm-85) cc_final: 0.8795 (tpp80) REVERT: A 532 LYS cc_start: 0.9284 (tptt) cc_final: 0.8907 (tppt) REVERT: A 659 ASP cc_start: 0.8837 (p0) cc_final: 0.8490 (p0) REVERT: A 706 ASN cc_start: 0.8620 (m-40) cc_final: 0.8367 (m-40) REVERT: A 719 GLU cc_start: 0.8418 (mp0) cc_final: 0.7720 (mp0) REVERT: A 760 GLN cc_start: 0.8902 (mp10) cc_final: 0.8477 (mp10) REVERT: A 815 TYR cc_start: 0.7145 (m-80) cc_final: 0.6342 (m-10) REVERT: A 926 MET cc_start: 0.7337 (tpt) cc_final: 0.7008 (tpt) REVERT: A 939 PHE cc_start: 0.6145 (OUTLIER) cc_final: 0.5435 (m-80) REVERT: A 961 PHE cc_start: 0.8513 (t80) cc_final: 0.8050 (t80) REVERT: B 41 GLN cc_start: 0.8882 (tt0) cc_final: 0.8270 (tt0) REVERT: B 253 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.8909 (tpp) REVERT: B 561 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8071 (ttp) REVERT: B 632 ASP cc_start: 0.8252 (t0) cc_final: 0.7952 (t0) REVERT: B 664 GLU cc_start: 0.5686 (OUTLIER) cc_final: 0.5147 (mp0) outliers start: 29 outliers final: 21 residues processed: 118 average time/residue: 0.6492 time to fit residues: 83.6660 Evaluate side-chains 122 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 630 CYS Chi-restraints excluded: chain B residue 646 PHE Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 665 ILE Chi-restraints excluded: chain B residue 705 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 139 optimal weight: 0.0570 chunk 156 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 91 optimal weight: 0.0970 chunk 7 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 overall best weight: 0.8698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 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 = 0.3648 r_free = 0.3648 target = 0.111929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.066761 restraints weight = 25162.946| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.93 r_work: 0.2768 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12875 Z= 0.129 Angle : 0.516 8.520 17546 Z= 0.250 Chirality : 0.043 0.280 1985 Planarity : 0.003 0.052 2280 Dihedral : 8.395 105.567 2197 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 31.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.04 % Favored : 93.84 % Rotamer: Outliers : 1.76 % Allowed : 12.11 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.22), residues: 1591 helix: 0.11 (0.43), residues: 155 sheet: 0.15 (0.23), residues: 513 loop : -0.74 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 473 TYR 0.010 0.001 TYR B 344 PHE 0.011 0.001 PHE B 481 TRP 0.009 0.001 TRP A 960 HIS 0.002 0.000 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00296 (12819) covalent geometry : angle 0.49426 (17415) SS BOND : bond 0.00259 ( 37) SS BOND : angle 1.15409 ( 74) hydrogen bonds : bond 0.02620 ( 397) hydrogen bonds : angle 5.84119 ( 1004) link_BETA1-4 : bond 0.00387 ( 10) link_BETA1-4 : angle 1.97962 ( 30) link_BETA1-6 : bond 0.00662 ( 1) link_BETA1-6 : angle 3.22682 ( 3) link_NAG-ASN : bond 0.00203 ( 8) link_NAG-ASN : angle 2.67787 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 THR cc_start: 0.9295 (p) cc_final: 0.9071 (p) REVERT: A 433 ARG cc_start: 0.9102 (mmm-85) cc_final: 0.8775 (tpp80) REVERT: A 532 LYS cc_start: 0.9274 (tptt) cc_final: 0.8896 (tppt) REVERT: A 547 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8282 (tmm160) REVERT: A 659 ASP cc_start: 0.8856 (p0) cc_final: 0.8501 (p0) REVERT: A 706 ASN cc_start: 0.8596 (m-40) cc_final: 0.8354 (m-40) REVERT: A 719 GLU cc_start: 0.8391 (mp0) cc_final: 0.7661 (mp0) REVERT: A 760 GLN cc_start: 0.8935 (mp10) cc_final: 0.8524 (mp10) REVERT: A 815 TYR cc_start: 0.7050 (m-80) cc_final: 0.6244 (m-10) REVERT: A 828 LEU cc_start: 0.8976 (tm) cc_final: 0.8736 (tm) REVERT: A 926 MET cc_start: 0.7325 (tpt) cc_final: 0.7026 (tpt) REVERT: A 939 PHE cc_start: 0.6240 (OUTLIER) cc_final: 0.5493 (m-80) REVERT: A 960 TRP cc_start: 0.7405 (t60) cc_final: 0.7153 (t60) REVERT: A 961 PHE cc_start: 0.8433 (t80) cc_final: 0.7945 (t80) REVERT: B 41 GLN cc_start: 0.8823 (tt0) cc_final: 0.8221 (tt0) REVERT: B 57 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6577 (tm) REVERT: B 253 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8788 (tpp) REVERT: B 561 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7995 (ttp) REVERT: B 632 ASP cc_start: 0.8285 (t0) cc_final: 0.7987 (t0) REVERT: B 664 GLU cc_start: 0.5697 (OUTLIER) cc_final: 0.5193 (mp0) outliers start: 24 outliers final: 18 residues processed: 115 average time/residue: 0.6023 time to fit residues: 75.5749 Evaluate side-chains 121 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 630 CYS Chi-restraints excluded: chain B residue 646 PHE Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 705 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 6 optimal weight: 0.9990 chunk 155 optimal weight: 20.0000 chunk 29 optimal weight: 0.0070 chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 112 optimal weight: 0.0270 chunk 47 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 151 optimal weight: 0.7980 chunk 63 optimal weight: 0.0980 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 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 = 0.3673 r_free = 0.3673 target = 0.113573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.067917 restraints weight = 32210.610| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.31 r_work: 0.2775 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12875 Z= 0.077 Angle : 0.484 8.297 17546 Z= 0.232 Chirality : 0.042 0.257 1985 Planarity : 0.003 0.053 2280 Dihedral : 8.083 106.101 2197 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 32.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.91 % Favored : 94.97 % Rotamer: Outliers : 1.69 % Allowed : 12.33 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.22), residues: 1591 helix: 0.43 (0.45), residues: 155 sheet: 0.33 (0.23), residues: 511 loop : -0.64 (0.22), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 473 TYR 0.009 0.001 TYR A 946 PHE 0.007 0.001 PHE A 750 TRP 0.011 0.001 TRP A 983 HIS 0.001 0.000 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00175 (12819) covalent geometry : angle 0.46384 (17415) SS BOND : bond 0.00149 ( 37) SS BOND : angle 0.94566 ( 74) hydrogen bonds : bond 0.02230 ( 397) hydrogen bonds : angle 5.55797 ( 1004) link_BETA1-4 : bond 0.00405 ( 10) link_BETA1-4 : angle 1.79828 ( 30) link_BETA1-6 : bond 0.00697 ( 1) link_BETA1-6 : angle 3.29871 ( 3) link_NAG-ASN : bond 0.00222 ( 8) link_NAG-ASN : angle 2.60960 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 THR cc_start: 0.9272 (p) cc_final: 0.9041 (p) REVERT: A 433 ARG cc_start: 0.9034 (mmm-85) cc_final: 0.8726 (tpp80) REVERT: A 532 LYS cc_start: 0.9244 (tptt) cc_final: 0.8878 (tppt) REVERT: A 547 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8193 (tmm160) REVERT: A 659 ASP cc_start: 0.8748 (p0) cc_final: 0.8397 (p0) REVERT: A 677 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7763 (mt-10) REVERT: A 706 ASN cc_start: 0.8559 (m-40) cc_final: 0.8318 (m-40) REVERT: A 719 GLU cc_start: 0.8345 (mp0) cc_final: 0.7592 (mp0) REVERT: A 760 GLN cc_start: 0.8965 (mp10) cc_final: 0.8541 (mp10) REVERT: A 815 TYR cc_start: 0.6843 (m-80) cc_final: 0.5946 (m-10) REVERT: A 828 LEU cc_start: 0.8959 (tm) cc_final: 0.8722 (tm) REVERT: A 926 MET cc_start: 0.7297 (tpt) cc_final: 0.6924 (tpt) REVERT: A 939 PHE cc_start: 0.6215 (OUTLIER) cc_final: 0.5590 (m-80) REVERT: A 960 TRP cc_start: 0.7383 (t60) cc_final: 0.7106 (t60) REVERT: A 961 PHE cc_start: 0.8399 (t80) cc_final: 0.7903 (t80) REVERT: B 41 GLN cc_start: 0.8788 (tt0) cc_final: 0.8189 (tt0) REVERT: B 204 TYR cc_start: 0.9071 (OUTLIER) cc_final: 0.8757 (p90) REVERT: B 253 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8751 (tpp) REVERT: B 561 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7960 (ttp) REVERT: B 632 ASP cc_start: 0.8233 (t0) cc_final: 0.7939 (t0) REVERT: B 664 GLU cc_start: 0.6033 (OUTLIER) cc_final: 0.5502 (mp0) outliers start: 23 outliers final: 15 residues processed: 116 average time/residue: 0.6416 time to fit residues: 81.0756 Evaluate side-chains 118 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 630 CYS Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 705 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 156 optimal weight: 20.0000 chunk 113 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.110486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.064679 restraints weight = 32726.633| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 3.31 r_work: 0.2716 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 12875 Z= 0.245 Angle : 0.576 9.686 17546 Z= 0.280 Chirality : 0.045 0.273 1985 Planarity : 0.004 0.052 2280 Dihedral : 7.988 95.681 2197 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 32.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.10 % Favored : 93.77 % Rotamer: Outliers : 1.83 % Allowed : 12.47 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.22), residues: 1591 helix: 0.08 (0.43), residues: 155 sheet: 0.23 (0.23), residues: 514 loop : -0.74 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 473 TYR 0.019 0.001 TYR B 683 PHE 0.012 0.001 PHE A 320 TRP 0.009 0.001 TRP B 264 HIS 0.004 0.001 HIS A 622 Details of bonding type rmsd covalent geometry : bond 0.00568 (12819) covalent geometry : angle 0.55564 (17415) SS BOND : bond 0.00318 ( 37) SS BOND : angle 1.26406 ( 74) hydrogen bonds : bond 0.03003 ( 397) hydrogen bonds : angle 5.80359 ( 1004) link_BETA1-4 : bond 0.00444 ( 10) link_BETA1-4 : angle 1.83618 ( 30) link_BETA1-6 : bond 0.00705 ( 1) link_BETA1-6 : angle 3.13131 ( 3) link_NAG-ASN : bond 0.00398 ( 8) link_NAG-ASN : angle 2.85826 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 THR cc_start: 0.9321 (p) cc_final: 0.9075 (p) REVERT: A 433 ARG cc_start: 0.9037 (mmm-85) cc_final: 0.8713 (tpp80) REVERT: A 532 LYS cc_start: 0.9230 (tptt) cc_final: 0.8835 (tppt) REVERT: A 547 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8260 (tmm160) REVERT: A 659 ASP cc_start: 0.8771 (p0) cc_final: 0.8430 (p0) REVERT: A 706 ASN cc_start: 0.8587 (m-40) cc_final: 0.8342 (m-40) REVERT: A 719 GLU cc_start: 0.8344 (mp0) cc_final: 0.7579 (mp0) REVERT: A 760 GLN cc_start: 0.8927 (mp10) cc_final: 0.8504 (mp10) REVERT: A 815 TYR cc_start: 0.6996 (m-80) cc_final: 0.6178 (m-10) REVERT: A 828 LEU cc_start: 0.8940 (tm) cc_final: 0.8719 (tm) REVERT: A 926 MET cc_start: 0.7337 (tpt) cc_final: 0.7054 (tpt) REVERT: A 960 TRP cc_start: 0.7321 (t60) cc_final: 0.7053 (t60) REVERT: A 961 PHE cc_start: 0.8472 (t80) cc_final: 0.7998 (t80) REVERT: B 41 GLN cc_start: 0.8765 (tt0) cc_final: 0.8100 (tt0) REVERT: B 253 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8825 (tpp) REVERT: B 561 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7991 (ttp) REVERT: B 632 ASP cc_start: 0.8280 (t0) cc_final: 0.7986 (t0) REVERT: B 664 GLU cc_start: 0.5949 (OUTLIER) cc_final: 0.5333 (mp0) outliers start: 25 outliers final: 17 residues processed: 116 average time/residue: 0.6179 time to fit residues: 78.1434 Evaluate side-chains 118 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 630 CYS Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 705 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 155 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 151 optimal weight: 0.2980 chunk 152 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 chunk 34 optimal weight: 0.0170 chunk 75 optimal weight: 0.0970 chunk 144 optimal weight: 0.0270 chunk 131 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.2474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 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 = 0.3667 r_free = 0.3667 target = 0.113089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.068004 restraints weight = 25995.613| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.98 r_work: 0.2786 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12875 Z= 0.075 Angle : 0.493 9.880 17546 Z= 0.236 Chirality : 0.042 0.235 1985 Planarity : 0.003 0.055 2280 Dihedral : 7.735 95.009 2197 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 33.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.16 % Favored : 94.72 % Rotamer: Outliers : 1.76 % Allowed : 12.69 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.22), residues: 1591 helix: 0.32 (0.44), residues: 155 sheet: 0.31 (0.23), residues: 508 loop : -0.64 (0.22), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 473 TYR 0.009 0.001 TYR A 946 PHE 0.008 0.001 PHE A 750 TRP 0.011 0.001 TRP A 266 HIS 0.001 0.000 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00172 (12819) covalent geometry : angle 0.47552 (17415) SS BOND : bond 0.00170 ( 37) SS BOND : angle 0.83797 ( 74) hydrogen bonds : bond 0.02320 ( 397) hydrogen bonds : angle 5.52438 ( 1004) link_BETA1-4 : bond 0.00414 ( 10) link_BETA1-4 : angle 1.60401 ( 30) link_BETA1-6 : bond 0.00704 ( 1) link_BETA1-6 : angle 3.28003 ( 3) link_NAG-ASN : bond 0.00210 ( 8) link_NAG-ASN : angle 2.64257 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 THR cc_start: 0.9262 (p) cc_final: 0.9032 (p) REVERT: A 433 ARG cc_start: 0.9130 (mmm-85) cc_final: 0.8823 (tpp80) REVERT: A 532 LYS cc_start: 0.9275 (tptt) cc_final: 0.8907 (tppt) REVERT: A 547 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8229 (tmm160) REVERT: A 659 ASP cc_start: 0.8766 (p0) cc_final: 0.8447 (p0) REVERT: A 677 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7891 (mt-10) REVERT: A 706 ASN cc_start: 0.8621 (m-40) cc_final: 0.8379 (m-40) REVERT: A 719 GLU cc_start: 0.8483 (mp0) cc_final: 0.7767 (mp0) REVERT: A 760 GLN cc_start: 0.8975 (mp10) cc_final: 0.8558 (mp10) REVERT: A 815 TYR cc_start: 0.7031 (m-80) cc_final: 0.6127 (m-10) REVERT: A 828 LEU cc_start: 0.8998 (tm) cc_final: 0.8758 (tm) REVERT: A 926 MET cc_start: 0.7364 (tpt) cc_final: 0.7096 (tpt) REVERT: A 960 TRP cc_start: 0.7397 (t60) cc_final: 0.7137 (t60) REVERT: A 961 PHE cc_start: 0.8396 (t80) cc_final: 0.7916 (t80) REVERT: B 41 GLN cc_start: 0.8876 (tt0) cc_final: 0.8285 (tt0) REVERT: B 204 TYR cc_start: 0.9103 (OUTLIER) cc_final: 0.8870 (p90) REVERT: B 253 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8861 (tpp) REVERT: B 410 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8371 (ptpp) REVERT: B 561 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7952 (ttp) REVERT: B 632 ASP cc_start: 0.8243 (t0) cc_final: 0.7958 (t0) REVERT: B 664 GLU cc_start: 0.6099 (OUTLIER) cc_final: 0.5541 (mp0) outliers start: 24 outliers final: 15 residues processed: 118 average time/residue: 0.6751 time to fit residues: 86.6612 Evaluate side-chains 117 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 630 CYS Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 705 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 147 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.110706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.065672 restraints weight = 24878.890| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.88 r_work: 0.2748 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 12875 Z= 0.221 Angle : 0.569 11.332 17546 Z= 0.276 Chirality : 0.043 0.209 1985 Planarity : 0.003 0.052 2280 Dihedral : 7.472 76.971 2197 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 33.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.29 % Favored : 93.58 % Rotamer: Outliers : 1.76 % Allowed : 12.47 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.22), residues: 1591 helix: 0.15 (0.43), residues: 155 sheet: 0.25 (0.23), residues: 514 loop : -0.69 (0.22), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 473 TYR 0.020 0.001 TYR B 683 PHE 0.011 0.001 PHE A 320 TRP 0.010 0.001 TRP A 141 HIS 0.004 0.001 HIS A 622 Details of bonding type rmsd covalent geometry : bond 0.00507 (12819) covalent geometry : angle 0.54524 (17415) SS BOND : bond 0.00288 ( 37) SS BOND : angle 1.44645 ( 74) hydrogen bonds : bond 0.02854 ( 397) hydrogen bonds : angle 5.71327 ( 1004) link_BETA1-4 : bond 0.00432 ( 10) link_BETA1-4 : angle 1.74380 ( 30) link_BETA1-6 : bond 0.00773 ( 1) link_BETA1-6 : angle 3.12922 ( 3) link_NAG-ASN : bond 0.00411 ( 8) link_NAG-ASN : angle 3.05717 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6131.58 seconds wall clock time: 105 minutes 10.63 seconds (6310.63 seconds total)